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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 278 Protein solution (5mcl): 14.5mg/ml TvNiR, 0.05M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystal was soaked in 0.1M KCN for 1h, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties Matthews coefficient Solvent content 4.23 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.56 α = 90 b = 194.56 β = 90 c = 194.56 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 2004-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81 EMBL/DESY, HAMBURG X11
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 1.55 12 99.9 0.047 40.1 4.9 350567 350257 25.1
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 1.55 1.57 100 0.421 3.9 4.8 11650
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 2OT4 1.55 11.98 332621 17636 99.66 0.14878 0.1481 0.1502 0.16175 0.1646 RANDOM 18.046
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 36.292 r_dihedral_angle_4_deg 18.014 r_dihedral_angle_3_deg 11.815 r_dihedral_angle_1_deg 6.109 r_scangle_it 3.228 r_scbond_it 2.138 r_angle_refined_deg 1.609 r_mcangle_it 1.497 r_angle_other_deg 0.977 r_mcbond_it 0.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.292 r_dihedral_angle_4_deg 18.014 r_dihedral_angle_3_deg 11.815 r_dihedral_angle_1_deg 6.109 r_scangle_it 3.228 r_scbond_it 2.138 r_angle_refined_deg 1.609 r_mcangle_it 1.497 r_angle_other_deg 0.977 r_mcbond_it 0.904 r_mcbond_other 0.249 r_chiral_restr 0.097 r_bond_refined_d 0.02 r_gen_planes_refined 0.016 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8217 Nucleic Acid Atoms Solvent Atoms 1218 Heterogen Atoms 826
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling