2VRC

Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.3M NAH2PO4,1.2M KH2PO4,0.2M NACL, 0.1M IMIDAZOLE(PH 8.0)
Crystal Properties
Matthews coefficientSolvent content
3.1761

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.957α = 90
b = 76.954β = 90
c = 272.826γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C1PAL/PLS6C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.5301000.0542.26.256316-2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5999.90.188.456

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 DIFFRACTIONSADTHROUGHOUTNONE2.529.365119627471000.1920.190.239RANDOM41.55
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]
-2.264.81-2.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.389
r_dihedral_angle_3_deg18.39
r_dihedral_angle_4_deg18.2
r_dihedral_angle_1_deg5.756
r_scangle_it3.325
r_scbond_it2.245
r_angle_refined_deg1.391
r_mcangle_it1.219
r_mcbond_it1.113
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.389
r_dihedral_angle_3_deg18.39
r_dihedral_angle_4_deg18.2
r_dihedral_angle_1_deg5.756
r_scangle_it3.325
r_scbond_it2.245
r_angle_refined_deg1.391
r_mcangle_it1.219
r_mcbond_it1.113
r_nbtor_refined0.313
r_nbd_refined0.222
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.191
r_xyhbond_nbd_refined0.143
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8647
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SOLVEphasing