X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7U07 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.1 M Sodium malonate, 0.1 M HEPES, 0.5% (v/v) Jaffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.9658.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.663α = 90
b = 105.663β = 90
c = 157.742γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.03317SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.35231000.3890.3950.0692.732.238007
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)
12.352.391004.2684.4011.0550.25616.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT7U072.3522.9834207179094.690.13730.13520.1793RANDOM39.108
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]
-2.65-2.655.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.981
r_dihedral_angle_4_deg17.881
r_dihedral_angle_3_deg15.487
r_dihedral_angle_1_deg5.684
r_rigid_bond_restr3.227
r_angle_refined_deg1.4
r_angle_other_deg1.27
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.981
r_dihedral_angle_4_deg17.881
r_dihedral_angle_3_deg15.487
r_dihedral_angle_1_deg5.684
r_rigid_bond_restr3.227
r_angle_refined_deg1.4
r_angle_other_deg1.27
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5094
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
PDB_EXTRACTdata extraction