X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
Crystal Properties
Matthews coefficientSolvent content
1.830

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.88α = 90
b = 59.79β = 90
c = 88.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

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
12.137.499.20.06513.43.3918109
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)
12.12.2297.10.4862.293.24

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 REPLACEMENTTHROUGHOUT4V2Y2.137.331720790199.680.181990.179470.23066RANDOM42.781
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]
0.341.28-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.585
r_dihedral_angle_4_deg15.214
r_dihedral_angle_3_deg13.623
r_long_range_B_refined6.092
r_long_range_B_other5.983
r_dihedral_angle_1_deg5.925
r_scangle_other2.531
r_mcangle_it1.942
r_mcangle_other1.941
r_scbond_it1.573
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.585
r_dihedral_angle_4_deg15.214
r_dihedral_angle_3_deg13.623
r_long_range_B_refined6.092
r_long_range_B_other5.983
r_dihedral_angle_1_deg5.925
r_scangle_other2.531
r_mcangle_it1.942
r_mcangle_other1.941
r_scbond_it1.573
r_scbond_other1.572
r_angle_refined_deg1.327
r_mcbond_it1.206
r_mcbond_other1.205
r_angle_other_deg1.023
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2158
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling