X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J49 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981 mM NADH, 10 mM oxamate, 100 mM sodium formate, 10% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.5965.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.69α = 90
b = 155.69β = 90
c = 230.011γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102013-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.237.498.80.1290.0450.99713.88.3161477
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3295.80.8050.2930.792.57.1

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 REPLACEMENTTHROUGHOUT1J492.237.4153341808098.840.172060.170650.19891RANDOM32.734
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]
0.080.080.08-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.505
r_dihedral_angle_4_deg22.622
r_dihedral_angle_3_deg15.104
r_long_range_B_refined7.348
r_long_range_B_other7.348
r_scangle_other5.773
r_dihedral_angle_1_deg5.709
r_scbond_it3.847
r_scbond_other3.847
r_mcangle_it3.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.505
r_dihedral_angle_4_deg22.622
r_dihedral_angle_3_deg15.104
r_long_range_B_refined7.348
r_long_range_B_other7.348
r_scangle_other5.773
r_dihedral_angle_1_deg5.709
r_scbond_it3.847
r_scbond_other3.847
r_mcangle_it3.183
r_mcangle_other3.183
r_mcbond_it2.295
r_mcbond_other2.295
r_angle_refined_deg1.857
r_angle_other_deg1.589
r_chiral_restr0.112
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.011
r_gen_planes_other0.009
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15290
Nucleic Acid Atoms
Solvent Atoms908
Heterogen Atoms366

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALAdata scaling
BUCCANEERmodel building