X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q18PDB ENTRY 2Q18

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.8293Na/K-phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5465.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.092α = 90
b = 157.092β = 90
c = 131.921γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2005-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.799.999.90.04930.75.5508045080481.7
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)
12.72.81000.5263.45.55043

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 ENTRY 2Q182.733.744800448004256299.10.240310.240310.238080.28355RANDOM63.124
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]
1.890.951.89-2.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.128
r_dihedral_angle_3_deg13.195
r_dihedral_angle_4_deg12.988
r_dihedral_angle_1_deg5.79
r_angle_refined_deg0.996
r_angle_other_deg0.709
r_scangle_it0.708
r_mcangle_it0.546
r_mcbond_it0.515
r_scbond_it0.451
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.128
r_dihedral_angle_3_deg13.195
r_dihedral_angle_4_deg12.988
r_dihedral_angle_1_deg5.79
r_angle_refined_deg0.996
r_angle_other_deg0.709
r_scangle_it0.708
r_mcangle_it0.546
r_mcbond_it0.515
r_scbond_it0.451
r_nbd_refined0.18
r_symmetry_vdw_other0.173
r_nbtor_refined0.165
r_nbd_other0.162
r_symmetry_vdw_refined0.128
r_xyhbond_nbd_refined0.126
r_nbtor_other0.075
r_chiral_restr0.058
r_symmetry_hbond_refined0.043
r_mcbond_other0.035
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9024
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing