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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OT4 PDB ENTRY 2OT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 278 Protein 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 coefficient Solvent content 4.49 72.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.56 α = 90 b = 196.56 β = 90 c = 196.56 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2007-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.998 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 19.9 97.8 0.096 10 226620
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.79 1.85 99.8 0.229 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OT4 1.8 19.9 215207 11413 97.7 0.1593 0.15862 0.1564 0.172 0.1698 RANDOM 18.146
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.191 r_dihedral_angle_4_deg 17.434 r_dihedral_angle_3_deg 12.348 r_dihedral_angle_1_deg 5.895 r_scangle_it 2.742 r_scbond_it 1.932 r_angle_refined_deg 1.529 r_mcangle_it 1.2 r_angle_other_deg 1.006 r_mcbond_it 0.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.191 r_dihedral_angle_4_deg 17.434 r_dihedral_angle_3_deg 12.348 r_dihedral_angle_1_deg 5.895 r_scangle_it 2.742 r_scbond_it 1.932 r_angle_refined_deg 1.529 r_mcangle_it 1.2 r_angle_other_deg 1.006 r_mcbond_it 0.859 r_symmetry_vdw_other 0.258 r_mcbond_other 0.235 r_nbd_refined 0.216 r_nbd_other 0.204 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.129 r_nbtor_other 0.106 r_symmetry_hbond_refined 0.1 r_xyhbond_nbd_refined 0.099 r_chiral_restr 0.098 r_metal_ion_refined 0.027 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8226 Nucleic Acid Atoms Solvent Atoms 1038 Heterogen Atoms 732
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement XDS data reduction XSCALE data scaling