3S7W | pdb_00003s7w

Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5278Protein solution (2.5mcl): 10.0 mg/ml TvNiRb, 0.05M Tris-HCl (pH7.2). Reservoir solution (2.5mcl): 1.26M tri-sodium citrate dihydrate, 0.09M HEPES/NaOH, 10% v/v glycerol, 0.1M hydroxylamine., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties
Matthews coefficientSolvent content
5.2471.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 194.89α = 90
b = 194.89β = 90
c = 194.89γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.812EMBL/DESY, HAMBURGX13

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
11.7919.797.20.07112.6223578
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)
11.791.8584.70.4492.7

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 2OT41.7919.72123541122497.60.154080.15310.160.172470.18RANDOM27.743
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_deg36.579
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg12.686
r_dihedral_angle_1_deg6.115
r_scangle_it3.178
r_scbond_it2.086
r_angle_refined_deg1.459
r_mcangle_it1.271
r_mcbond_it0.718
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.579
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg12.686
r_dihedral_angle_1_deg6.115
r_scangle_it3.178
r_scbond_it2.086
r_angle_refined_deg1.459
r_mcangle_it1.271
r_mcbond_it0.718
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.014
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 Atoms8229
Nucleic Acid Atoms
Solvent Atoms1088
Heterogen Atoms744

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling