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Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine
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 7.5 278 Protein 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 coefficient Solvent content 5.24 71.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.89 α = 90 b = 194.89 β = 90 c = 194.89 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 2009-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.812 EMBL/DESY, HAMBURG X13
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 1.79 19.7 97.2 0.071 12.6 223578
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 1.79 1.85 84.7 0.449 2.7
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 1.79 19.7 212354 11224 97.6 0.15408 0.1531 0.1579 0.17247 0.1767 RANDOM 27.743
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.579 r_dihedral_angle_4_deg 16.672 r_dihedral_angle_3_deg 12.686 r_dihedral_angle_1_deg 6.115 r_scangle_it 3.178 r_scbond_it 2.086 r_angle_refined_deg 1.459 r_mcangle_it 1.271 r_mcbond_it 0.718 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.579 r_dihedral_angle_4_deg 16.672 r_dihedral_angle_3_deg 12.686 r_dihedral_angle_1_deg 6.115 r_scangle_it 3.178 r_scbond_it 2.086 r_angle_refined_deg 1.459 r_mcangle_it 1.271 r_mcbond_it 0.718 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 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 Atoms Number Protein Atoms 8229 Nucleic Acid Atoms Solvent Atoms 1088 Heterogen Atoms 744
Software Software Software Name Purpose DNA data collection REFMAC refinement XDS data reduction XSCALE data scaling