X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OXU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62911.5M sodium potassium phosphate pH 5.6, 3% MPD Soaking: 19.5% hexane, 36 hours, cryoprotected with 25% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.3647.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.106α = 90
b = 57.961β = 109.17
c = 60.801γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291PIXELDECTRIS PILATUS 6MMIRRORS KB2020-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979260ALBAXALOC

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
11.8244.9399.90.2670.2940.126.76.230212
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.8699.90.7070.7730.3072.86.4

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5OXU1.8244.9728677151999.880.22240.21990.2694RANDOM20.223
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]
-1.221.53-1.461.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.253
r_dihedral_angle_4_deg15.316
r_dihedral_angle_3_deg12.759
r_dihedral_angle_1_deg6.638
r_angle_refined_deg1.38
r_angle_other_deg1.322
r_chiral_restr0.067
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.253
r_dihedral_angle_4_deg15.316
r_dihedral_angle_3_deg12.759
r_dihedral_angle_1_deg6.638
r_angle_refined_deg1.38
r_angle_other_deg1.322
r_chiral_restr0.067
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2517
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing