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M144L mutant of Nitrite Reductase from Alcaligenes xylosoxidans in space group P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BO0 PDB ENTRY 2BO0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 pH 4.20
Crystal Properties Matthews coefficient Solvent content 5.89 79.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.958 α = 90 b = 175.91 β = 90 c = 181.056 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 100 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 2.4 49.8 98.5 0.08 16.7 5.2 213297
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 2.4 2.5 71 0.45 2.2 4.1
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BO0 2.4 49.7 199329 10571 97.6 0.172 0.171 0.193 RANDOM 47.77
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] 0.56 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_4_deg 18.395 r_dihedral_angle_3_deg 13.93 r_dihedral_angle_1_deg 6.779 r_scangle_it 2.074 r_scbond_it 1.289 r_angle_refined_deg 1.242 r_mcangle_it 0.715 r_mcbond_it 0.455 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_4_deg 18.395 r_dihedral_angle_3_deg 13.93 r_dihedral_angle_1_deg 6.779 r_scangle_it 2.074 r_scbond_it 1.289 r_angle_refined_deg 1.242 r_mcangle_it 0.715 r_mcbond_it 0.455 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.083 r_bond_refined_d 0.009 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_xyhbond_nbd_other r_metal_ion_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15315 Nucleic Acid Atoms Solvent Atoms 1282 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing