3RKH | pdb_00003rkh

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OT4PDB ENTRY 2OT4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP278Protein solution (2.5 uL): 11.6 mg/mL TvNiR, 0.05 M Tris-HCl, pH 8.0, reservoir solution (2.5 uL): 0.2 M ammonium acetate, 0.1 M citric acid trisodium salt, pH 5.6, 30% MPD, 0.1 M sodium nitrite, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties
Matthews coefficientSolvent content
5.06689175.724762

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.8α = 90
b = 192.8β = 90
c = 192.8γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.4KURCHATOV SNCK4.4

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
11.83136.3399.80.122020815326.2
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)
11.831.999.90.6713.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2OT41.831001976471046699.850.142390.141370.140.161960.16RANDOM21.013
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.999
r_dihedral_angle_4_deg18.945
r_dihedral_angle_3_deg12.468
r_dihedral_angle_1_deg6.294
r_scangle_it3.544
r_scbond_it2.325
r_angle_refined_deg1.7
r_mcangle_it1.498
r_mcbond_it0.874
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.999
r_dihedral_angle_4_deg18.945
r_dihedral_angle_3_deg12.468
r_dihedral_angle_1_deg6.294
r_scangle_it3.544
r_scbond_it2.325
r_angle_refined_deg1.7
r_mcangle_it1.498
r_mcbond_it0.874
r_chiral_restr0.11
r_bond_refined_d0.02
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8239
Nucleic Acid Atoms
Solvent Atoms1327
Heterogen Atoms712

Software

Software
Software NamePurpose
AUTOMARdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling