X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GOLPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 1DVVPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 1X0JPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 3DAIPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 3HMHPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 2GRCPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 2OO1PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 2OSSPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 3D7CPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental modelPDB 3DWYPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.427722% PEG3350, 0.1 M Tris, pH 8.4, 0.25 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.4764.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.417α = 90
b = 95.417β = 90
c = 33.054γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9686DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7627.561000.0630.021209.9173921739230.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.861000.850.852.69.72512

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY1.7627.56165011650188099.960.1780.1780.175980.21719RANDOM39.299
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.540.540.54-1.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.646
r_dihedral_angle_4_deg19.661
r_dihedral_angle_3_deg13.736
r_long_range_B_other11.192
r_long_range_B_refined11.147
r_scangle_other10.348
r_scbond_other9.763
r_scbond_it9.745
r_mcangle_it6.693
r_mcangle_other6.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.646
r_dihedral_angle_4_deg19.661
r_dihedral_angle_3_deg13.736
r_long_range_B_other11.192
r_long_range_B_refined11.147
r_scangle_other10.348
r_scbond_other9.763
r_scbond_it9.745
r_mcangle_it6.693
r_mcangle_other6.69
r_mcbond_it5.779
r_mcbond_other5.727
r_dihedral_angle_1_deg5.359
r_angle_refined_deg1.624
r_angle_other_deg0.893
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms829
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms17

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling