X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.5 M (NH4)H2PO4
Crystal Properties
Matthews coefficientSolvent content
1.8433.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.562α = 90
b = 60.162β = 90
c = 88.406γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-03-09MSINGLE 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)Rrim 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
11.5244.2499.90.0660.0690.99918.961247297
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.6199.41.3371.3920.78312

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 REPLACEMENTTHROUGHOUT4v2y1.5244.2444930236799.850.18610.18450.2169RANDOM28.883
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]
-0.721.84-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.249
r_dihedral_angle_3_deg13.644
r_dihedral_angle_4_deg12.116
r_dihedral_angle_1_deg7.006
r_angle_refined_deg1.862
r_angle_other_deg1.508
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.249
r_dihedral_angle_3_deg13.644
r_dihedral_angle_4_deg12.116
r_dihedral_angle_1_deg7.006
r_angle_refined_deg1.862
r_angle_other_deg1.508
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2481
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing