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Nitrite bound copper containing nitrite reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J9Q PDB entry 1J9Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 PEG 4000, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 321K
Crystal Properties Matthews coefficient Solvent content 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.6 α = 90 b = 102.45 β = 90 c = 145.98 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 IMAGE PLATE MAR scanner 345 mm plate 2002-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
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 1.4 25 97.3 0.041 21 7.3 1173705 1173705
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) 1.4 1.45 93.4 0.121
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1J9Q 1.4 24.85 167035 9856 100 0.11465 0.11326 0.13846 RANDOM 12.49
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] 0.03 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.331 r_scangle_it 3.785 r_scbond_it 2.52 r_mcangle_it 1.616 r_angle_refined_deg 1.398 r_mcbond_it 1.063 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.268 r_symmetry_vdw_refined 0.255 r_nbd_other 0.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.331 r_scangle_it 3.785 r_scbond_it 2.52 r_mcangle_it 1.616 r_angle_refined_deg 1.398 r_mcbond_it 1.063 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.268 r_symmetry_vdw_refined 0.255 r_nbd_other 0.252 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.09 r_nbtor_other 0.08 r_gen_planes_other 0.016 r_gen_planes_refined 0.011 r_bond_refined_d 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7708 Nucleic Acid Atoms Solvent Atoms 1144 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling