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Crystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase with nitrite bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OE1 PDB ENTRY 1OE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 CRYSTALS OF HIS313GLN NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML RESERVOIR. CRYSTALS OF BOTH MUTANTS WERE AN INTENSE BLUE COLOUR AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY. FOR HIS313GLN_NO2.-, 10MM SODIUM NITRITE WAS ADDED TO THE RESERVOIR SOLUTION PRIOR TO CRYSTALLISATION.
Crystal Properties Matthews coefficient Solvent content 3.05 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.641 α = 90 b = 89.641 β = 90 c = 143.569 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 MIRRORS 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 1.72 60 97.5 0.09 8.7 44676 18.8
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 1.72 1.75 98.4 0.42 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OE1 1.72 37.53 44676 2257 97.5 0.182 0.18 0.1889 0.21 0.1998 RANDOM 22.72
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] 0.57 0.28 0.57 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.171 r_scangle_it 2.676 r_scbond_it 1.718 r_angle_refined_deg 1.444 r_mcangle_it 1.128 r_angle_other_deg 0.945 r_mcbond_it 0.653 r_symmetry_vdw_other 0.294 r_nbd_other 0.253 r_nbd_refined 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.171 r_scangle_it 2.676 r_scbond_it 1.718 r_angle_refined_deg 1.444 r_mcangle_it 1.128 r_angle_other_deg 0.945 r_mcbond_it 0.653 r_symmetry_vdw_other 0.294 r_nbd_other 0.253 r_nbd_refined 0.234 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.155 r_chiral_restr 0.085 r_nbtor_other 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_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 2523 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing