3GM6 | pdb_00003gm6

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5278Protein solution (2.5mcl): 9.3mg/ml TvNiR, 0.1M potassium phosphate (pH7.0). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4-pentanediol (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties
Matthews coefficientSolvent content
4.4972.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.56α = 90
b = 196.56β = 90
c = 196.56γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.998KURCHATOV 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
11.819.997.80.09610226620
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)
1.791.8599.80.2294.9

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 2OT41.819.92152071141397.70.15930.158620.170.1720.18RANDOM18.146
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_deg36.191
r_dihedral_angle_4_deg17.434
r_dihedral_angle_3_deg12.348
r_dihedral_angle_1_deg5.895
r_scangle_it2.742
r_scbond_it1.932
r_angle_refined_deg1.529
r_mcangle_it1.2
r_angle_other_deg1.006
r_mcbond_it0.859
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.191
r_dihedral_angle_4_deg17.434
r_dihedral_angle_3_deg12.348
r_dihedral_angle_1_deg5.895
r_scangle_it2.742
r_scbond_it1.932
r_angle_refined_deg1.529
r_mcangle_it1.2
r_angle_other_deg1.006
r_mcbond_it0.859
r_symmetry_vdw_other0.258
r_mcbond_other0.235
r_nbd_refined0.216
r_nbd_other0.204
r_nbtor_refined0.188
r_symmetry_vdw_refined0.129
r_nbtor_other0.106
r_symmetry_hbond_refined0.1
r_xyhbond_nbd_refined0.099
r_chiral_restr0.098
r_metal_ion_refined0.027
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8226
Nucleic Acid Atoms
Solvent Atoms1038
Heterogen Atoms732

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling