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Cu-containing nitrite reductase at pH 6.0 with bound nitrite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZV2 PDB ENTRY 1ZV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 Tris, MgCl2, NaNO2, PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.74 α = 90 b = 74.74 β = 90 c = 153.146 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 MAR CCD 165 mm 2005-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 24.71 99.3 0.06 0.06 7.2 3.2 24972
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.363 0.363 1.8 3.1 3664
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 (All) 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 1ZV2 1.9 24.71 24965 1270 99.21 0.201 0.199 0.2001 0.235 0.236 RANDOM 33.106
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] -1.55 -0.78 -1.55 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.707 r_dihedral_angle_4_deg 18.564 r_dihedral_angle_3_deg 14.444 r_dihedral_angle_1_deg 7.642 r_scangle_it 3.304 r_scbond_it 2.507 r_angle_refined_deg 1.878 r_mcangle_it 1.622 r_mcbond_it 1.131 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.707 r_dihedral_angle_4_deg 18.564 r_dihedral_angle_3_deg 14.444 r_dihedral_angle_1_deg 7.642 r_scangle_it 3.304 r_scbond_it 2.507 r_angle_refined_deg 1.878 r_mcangle_it 1.622 r_mcbond_it 1.131 r_nbtor_refined 0.319 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.133 r_symmetry_metal_ion_refined 0.04 r_metal_ion_refined 0.032 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2530 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing