X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292Protein: 12.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3. Screen: JCSG+ (F8), 2.1M DL-Malic acid pH 7.0; Cryo: 25% PEG 400, 1.5M DL-Malic acid pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.8556.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.928α = 90
b = 62.022β = 90
c = 101.916γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe2019-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.83301000.0840.0840.0930.040.99919.45.468046-320.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.861000.7730.7730.8570.3670.782.25.4

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 REPLACEMENTTHROUGHOUT7kom1.8329.864577342299.680.16350.16190.1933RANDOM23.732
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]
-1.27-1.092.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.694
r_dihedral_angle_4_deg15.261
r_dihedral_angle_3_deg9.97
r_dihedral_angle_1_deg4.426
r_angle_refined_deg1.364
r_angle_other_deg0.358
r_chiral_restr0.062
r_gen_planes_refined0.056
r_gen_planes_other0.053
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.694
r_dihedral_angle_4_deg15.261
r_dihedral_angle_3_deg9.97
r_dihedral_angle_1_deg4.426
r_angle_refined_deg1.364
r_angle_other_deg0.358
r_chiral_restr0.062
r_gen_planes_refined0.056
r_gen_planes_other0.053
r_bond_refined_d0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4546
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing