X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5L3Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293
Crystal Properties
Matthews coefficientSolvent content
2.3748.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.95α = 90
b = 64.84β = 105.52
c = 91.48γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.954.8899.10.0870.0940.0350.99913.67.147271
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9597.51.996.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5L3Z1.954.8844913235799.130.19630.19460.2291RANDOM49.185
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]
0.282.86-1.74-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.648
r_dihedral_angle_4_deg15.16
r_dihedral_angle_3_deg13.676
r_dihedral_angle_1_deg6.345
r_mcangle_it1.864
r_angle_refined_deg1.294
r_mcbond_it1.185
r_mcbond_other1.185
r_angle_other_deg0.907
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.648
r_dihedral_angle_4_deg15.16
r_dihedral_angle_3_deg13.676
r_dihedral_angle_1_deg6.345
r_mcangle_it1.864
r_angle_refined_deg1.294
r_mcbond_it1.185
r_mcbond_other1.185
r_angle_other_deg0.907
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4075
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms13

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
XDSdata scaling