X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2940.4 M Ammonium phosphate
Crystal Properties
Matthews coefficientSolvent content
1.831.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.656α = 90
b = 59.02β = 90
c = 88.593γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-14MSINGLE 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)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
11.549.1299.50.11114.2912.648555
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5997.20.790.872.3212.6

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 REPLACEMENTTHROUGHOUT4v2y1.549.1246128242799.520.194630.193540.21537RANDOM24.005
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]
-0.310.78-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg13.651
r_dihedral_angle_3_deg12.755
r_dihedral_angle_1_deg6.149
r_long_range_B_refined4.832
r_long_range_B_other4.81
r_scangle_other1.825
r_angle_refined_deg1.81
r_mcangle_it1.779
r_mcangle_other1.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg13.651
r_dihedral_angle_3_deg12.755
r_dihedral_angle_1_deg6.149
r_long_range_B_refined4.832
r_long_range_B_other4.81
r_scangle_other1.825
r_angle_refined_deg1.81
r_mcangle_it1.779
r_mcangle_other1.779
r_scbond_it1.085
r_scbond_other1.084
r_angle_other_deg1.015
r_mcbond_it1.01
r_mcbond_other1.009
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms2540
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling