X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VB8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1 M MES pH 6.5, 0.2 M ammonium sulphate, 30% (w/v) polyethylene glycol monomethyl ether 5000
Crystal Properties
Matthews coefficientSolvent content
2.1542.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.485α = 90
b = 111.733β = 90
c = 131.102γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2020-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.978530SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.5548.95699.90.1180.1270.0480.99916.313.24686452.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.562.651001.1561.2470.4680.9022.413.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7VB82.5648.95646802236899.9320.190.18640.256765.847
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]
-6.5870.5166.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.694
r_dihedral_angle_3_deg19.332
r_dihedral_angle_6_deg15.446
r_lrange_it12.62
r_lrange_other12.62
r_scangle_it10.459
r_scangle_other10.458
r_mcangle_it9.851
r_mcangle_other9.851
r_dihedral_angle_1_deg8.285
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.694
r_dihedral_angle_3_deg19.332
r_dihedral_angle_6_deg15.446
r_lrange_it12.62
r_lrange_other12.62
r_scangle_it10.459
r_scangle_other10.458
r_mcangle_it9.851
r_mcangle_other9.851
r_dihedral_angle_1_deg8.285
r_scbond_it7.85
r_scbond_other7.849
r_mcbond_it7.051
r_mcbond_other7.05
r_angle_refined_deg2.381
r_angle_other_deg0.79
r_nbd_refined0.238
r_symmetry_nbd_other0.206
r_nbtor_refined0.189
r_nbd_other0.188
r_symmetry_nbd_refined0.182
r_xyhbond_nbd_refined0.18
r_symmetry_xyhbond_nbd_other0.142
r_ncsr_local_group_50.139
r_ncsr_local_group_30.138
r_ncsr_local_group_40.138
r_ncsr_local_group_20.135
r_ncsr_local_group_10.133
r_ncsr_local_group_60.13
r_symmetry_xyhbond_nbd_refined0.119
r_chiral_restr0.102
r_symmetry_nbtor_other0.092
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11270
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing