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
1.7730.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.455α = 90
b = 58.824β = 90
c = 88.234γ = 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
11.5544.1299.80.090.99915.0912.6643510
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)
11.551.6498.90.980.85

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 REPLACEMENTTHROUGHOUT4v2y1.5544.1241337217399.780.188150.186850.21293RANDOM28.054
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]
-0.470.99-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.472
r_dihedral_angle_3_deg12.963
r_dihedral_angle_4_deg12.044
r_dihedral_angle_1_deg6.3
r_long_range_B_refined4.507
r_long_range_B_other4.507
r_scangle_other2.231
r_mcangle_it1.925
r_mcangle_other1.924
r_angle_refined_deg1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.472
r_dihedral_angle_3_deg12.963
r_dihedral_angle_4_deg12.044
r_dihedral_angle_1_deg6.3
r_long_range_B_refined4.507
r_long_range_B_other4.507
r_scangle_other2.231
r_mcangle_it1.925
r_mcangle_other1.924
r_angle_refined_deg1.78
r_scbond_it1.364
r_scbond_other1.364
r_mcbond_it1.132
r_mcbond_other1.131
r_angle_other_deg1.017
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms2516
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling