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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)
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 8.7 278 Protein solution (2.5 uL): 9.3 mg/mL TvNiRb, 0.1 M potassium phosphate, pH 7.0, Reservoir solution (2.5 uL): 0.2 M tri-sodium citrate dihydrate, 0.1 M Tris hydrochloride, pH8.5, 30% v/v PEG400 , VAPOR DIFFUSION, HANGING DROP, temperature 278.0 K
Crystal Properties Matthews coefficient Solvent content 5.09 75.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193 α = 90 b = 193 β = 90 c = 193 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU SPring-8 BL41XU
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 1.45 136.472 99.9 0.11 11.1 464187 21.2
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 1.45 1.6 99.9 0.544 3.4
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 1.45 100 397225 20931 99.91 0.12468 0.12385 0.1339 0.14041 0.148 RANDOM 14.342
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 36.488 r_dihedral_angle_4_deg 16.519 r_dihedral_angle_3_deg 11.959 r_sphericity_free 7.429 r_dihedral_angle_1_deg 6.122 r_scangle_it 4.415 r_sphericity_bonded 4.147 r_scbond_it 2.963 r_mcangle_it 1.981 r_rigid_bond_restr 1.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 16.519 r_dihedral_angle_3_deg 11.959 r_sphericity_free 7.429 r_dihedral_angle_1_deg 6.122 r_scangle_it 4.415 r_sphericity_bonded 4.147 r_scbond_it 2.963 r_mcangle_it 1.981 r_rigid_bond_restr 1.794 r_angle_refined_deg 1.46 r_mcbond_it 1.216 r_angle_other_deg 1.098 r_mcbond_other 0.648 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8231 Nucleic Acid Atoms Solvent Atoms 1186 Heterogen Atoms 867
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling