☰ Navigation Tabs
Met62Leu variant of nitrite reductase from Alcaligenes faeclis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SJM PDB entry 1SJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 298 pH 4.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.132 α = 90 b = 102.223 β = 90 c = 146.145 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 84.52 50095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 84.52
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Refinement of wild-type structure THROUGHOUT PDB entry 1SJM 2.1 84.52 50095 50095 2688 97.25 0.1695 0.1664 0.22698 0.231 RANDOM 24.203
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] 1.8 -1.34 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_3_deg 13.686 r_dihedral_angle_1_deg 6.977 r_scangle_it 2.141 r_scbond_it 1.391 r_angle_refined_deg 1.282 r_mcangle_it 0.889 r_mcbond_it 0.54 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_3_deg 13.686 r_dihedral_angle_1_deg 6.977 r_scangle_it 2.141 r_scbond_it 1.391 r_angle_refined_deg 1.282 r_mcangle_it 0.889 r_mcbond_it 0.54 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.185 r_xyhbond_nbd_other 0.178 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.086 r_metal_ion_refined 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_metal_ion_other r_symmetry_vdw_other 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 7683 Nucleic Acid Atoms Solvent Atoms 1092 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement