X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VA7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52952,2'-disulfanediylbis(N-(2-(1H-indol-3-yl)ethyl)ethan-1-amine), NADP+, MES, PEG4000, MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.244.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.64α = 90
b = 87.86β = 90
c = 160.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat Si Rh coated Mirror2021-05-31MSINGLE 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)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
12.938.9999.90.1990.2080.99913.7113.0622410979.84
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.981002.8662.9780.6711.5113.581

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 REPLACEMENTTHROUGHOUT6va72.938.9922903120699.920.21060.20580.3018RANDOM77.492
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]
3.85-2.64-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_3_deg21.517
r_dihedral_angle_4_deg18.115
r_dihedral_angle_1_deg8.001
r_angle_refined_deg1.489
r_angle_other_deg1.145
r_chiral_restr0.063
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_3_deg21.517
r_dihedral_angle_4_deg18.115
r_dihedral_angle_1_deg8.001
r_angle_refined_deg1.489
r_angle_other_deg1.145
r_chiral_restr0.063
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7158
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms96

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing