X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JRO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629720 % PEG3350 0.2 M Na malonate pH 6.0 12.5 mM NADH added to the protein solution prior to drop mixing
Crystal Properties
Matthews coefficientSolvent content
3.240.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.109α = 90
b = 255.316β = 90
c = 262.312γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6MToroidal mirrors2016-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97625ESRFID23-1

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
12.548.9699.30.0750.0960.0440.99710.24.39204546.1
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)
12.52.5499.50.6060.7790.3690.7392.14.4

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 REPLACEMENTTHROUGHOUT4JRO2.53087489450899.130.19270.19170.2106RANDOM55.47
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]
-0.150.74-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.667
r_dihedral_angle_4_deg18.605
r_dihedral_angle_3_deg13.841
r_dihedral_angle_1_deg5.485
r_angle_refined_deg1.478
r_angle_other_deg0.938
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.667
r_dihedral_angle_4_deg18.605
r_dihedral_angle_3_deg13.841
r_dihedral_angle_1_deg5.485
r_angle_refined_deg1.478
r_angle_other_deg0.938
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14288
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms475

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing