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Nitrite Reductase from Alcaligenes xylosoxidans
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 6.5 100 MM MES PH 6.5, 10 MM ZNSO4 AND 25 % PEG-MME 550
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.451 α = 90 b = 89.451 β = 90 c = 144.473 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 IMAGE PLATE RIGAKU IMAGE PLATE OSMIC BLUE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.35 34.1 100 0.05 25.9 5.4 17939
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 2.35 2.41 100 0.32 4.6 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OE1 2.35 34.14 17023 916 100 0.167 0.165 0.1663 0.215 0.2173 RANDOM 38.97
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] -0.02 -0.01 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.854 r_dihedral_angle_4_deg 20.189 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_1_deg 7.271 r_scangle_it 2.711 r_scbond_it 1.821 r_angle_refined_deg 1.539 r_mcangle_it 1.282 r_mcbond_it 0.788 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.854 r_dihedral_angle_4_deg 20.189 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_1_deg 7.271 r_scangle_it 2.711 r_scbond_it 1.821 r_angle_refined_deg 1.539 r_mcangle_it 1.282 r_mcbond_it 0.788 r_nbtor_refined 0.305 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 2548 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing