X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72931.1 M Sodium malonate, 0.1 M HEPES, 0.5% (v/v) Jaffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
3.160.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.401α = 90
b = 106.401β = 90
c = 159.643γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

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
12.537.651000.290.2960.0570.99812.826.132478
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)
12.52.61005.5235.6411.1380.44524

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 SYNTHESISTHROUGHOUT7U072.537.6530621163399.450.15380.15120.2017RANDOM54.753
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]
-2.33-2.334.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.431
r_dihedral_angle_4_deg17.865
r_dihedral_angle_3_deg17.269
r_dihedral_angle_1_deg5.963
r_rigid_bond_restr1.59
r_angle_refined_deg1.347
r_angle_other_deg1.266
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.431
r_dihedral_angle_4_deg17.865
r_dihedral_angle_3_deg17.269
r_dihedral_angle_1_deg5.963
r_rigid_bond_restr1.59
r_angle_refined_deg1.347
r_angle_other_deg1.266
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5082
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling