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 Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.417α = 90
b = 58.795β = 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
11.7348.9398.80.14110.5512.4630720
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)
11.731.8492.40.890.8611.99

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 REPLACEMENTTHROUGHOUT4v2y1.7448.9329052153099.730.177030.174050.23398RANDOM34.965
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]
-0.841.95-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.994
r_dihedral_angle_4_deg14.944
r_dihedral_angle_3_deg12.957
r_dihedral_angle_1_deg7.161
r_long_range_B_refined6.191
r_long_range_B_other6.177
r_scangle_other4.287
r_mcangle_other3.326
r_mcangle_it3.324
r_scbond_it2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.994
r_dihedral_angle_4_deg14.944
r_dihedral_angle_3_deg12.957
r_dihedral_angle_1_deg7.161
r_long_range_B_refined6.191
r_long_range_B_other6.177
r_scangle_other4.287
r_mcangle_other3.326
r_mcangle_it3.324
r_scbond_it2.86
r_scbond_other2.859
r_mcbond_it2.27
r_mcbond_other2.266
r_angle_refined_deg2.259
r_angle_other_deg1.213
r_chiral_restr0.174
r_bond_refined_d0.026
r_gen_planes_refined0.015
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 Atoms2505
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing