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Crystal structure of H129V Mutant of Alcaligenes Xylosoxidans Nitrite Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NDT PDB ENTRY 1NDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 100MM MES BUFFER PH 6.5 200MM ZNSO4, 40-50% PEG550 MME
Crystal Properties Matthews coefficient Solvent content 3.2 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.206 α = 90 b = 91.206 β = 90 c = 145.866 γ = 120
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 2001-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.95 30 99.7 0.05 22 3.5 35547
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 1.95 1.99 99.9 0.4 2.5 3
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NDT 1.95 30.01 31259 1670 99.8 0.202 0.201 0.226 0.2401 RANDOM 30.52
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] 0.99 0.49 0.99 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.127 r_dihedral_angle_1_deg 5.211 r_scangle_it 2.728 r_scbond_it 1.698 r_angle_refined_deg 1.683 r_mcangle_it 1.191 r_symmetry_hbond_refined 0.921 r_angle_other_deg 0.882 r_mcbond_it 0.681 r_nbd_other 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.127 r_dihedral_angle_1_deg 5.211 r_scangle_it 2.728 r_scbond_it 1.698 r_angle_refined_deg 1.683 r_mcangle_it 1.191 r_symmetry_hbond_refined 0.921 r_angle_other_deg 0.882 r_mcbond_it 0.681 r_nbd_other 0.218 r_nbd_refined 0.214 r_symmetry_vdw_other 0.18 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.101 r_nbtor_other 0.064 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2545 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing