X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VA8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION295PEG8K
Crystal Properties
Matthews coefficientSolvent content
5.9679.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.73α = 90
b = 157.73β = 90
c = 113.82γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16MFlat side-deflecting, Rh-coated Si mirror2021-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-10.97946SSRLBL12-1

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
13.6539.4399.90.2130.2170.99915.326.58816483120.317
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)
13.653.741002.7452.7960.6321.6527.375

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 REPLACEMENTTHROUGHOUT6va83.6539.431565882599.870.19350.19130.2352RANDOM138.286
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]
0.030.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.153
r_dihedral_angle_3_deg20.193
r_dihedral_angle_4_deg18.959
r_dihedral_angle_1_deg8.735
r_angle_refined_deg1.733
r_angle_other_deg1.222
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.153
r_dihedral_angle_3_deg20.193
r_dihedral_angle_4_deg18.959
r_dihedral_angle_1_deg8.735
r_angle_refined_deg1.733
r_angle_other_deg1.222
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3439
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing