X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6292Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen (AmSO4, H2): 0.1M Sodium acetate pH 4.6, 2.0M Ammonium sulfate; Cryo: 25% Sucrose, 2.0M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.9769

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.349α = 90
b = 203.349β = 90
c = 157.775γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBE2019-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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)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
12.7301000.090.090.0980.03820.36.6103165-355.2
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)
12.72.751000.790.790.8570.3320.7372.46.7

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 REPLACEMENTTHROUGHOUT2ehj2.729.7197876520399.880.19030.18880.2187RANDOM55.587
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]
-0.03-0.02-0.030.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg9.326
r_dihedral_angle_4_deg6.792
r_dihedral_angle_3_deg5.445
r_angle_refined_deg1.167
r_dihedral_angle_1_deg1.159
r_angle_other_deg0.291
r_gen_planes_refined0.054
r_gen_planes_other0.053
r_chiral_restr0.05
r_bond_refined_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg9.326
r_dihedral_angle_4_deg6.792
r_dihedral_angle_3_deg5.445
r_angle_refined_deg1.167
r_dihedral_angle_1_deg1.159
r_angle_other_deg0.291
r_gen_planes_refined0.054
r_gen_planes_other0.053
r_chiral_restr0.05
r_bond_refined_d0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15854
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms561

Software

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