X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QCB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42982.0 M Ammonium Sulfate, 0.1 M Sodium Acetate pH 4
Crystal Properties
Matthews coefficientSolvent content
2.1642.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.644α = 90
b = 57.644β = 90
c = 171.909γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21ALS5.0.2

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
11.3540.761000.0320.0330.009138.313.732429
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)
11.351.3799.90.9771.0160.2750.87913.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2QCB1.3540.6730695169499.950.21730.2160.2415RANDOM23.045
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]
0.560.56-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg32.653
r_dihedral_angle_2_deg25.048
r_dihedral_angle_3_deg14.922
r_dihedral_angle_1_deg8.096
r_angle_refined_deg2.116
r_angle_other_deg1.637
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg32.653
r_dihedral_angle_2_deg25.048
r_dihedral_angle_3_deg14.922
r_dihedral_angle_1_deg8.096
r_angle_refined_deg2.116
r_angle_other_deg1.637
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms937
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing