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Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG 3350, potassium chloride
Crystal Properties Matthews coefficient Solvent content 3.46 64.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.226 α = 90 b = 153.226 β = 90 c = 153.226 γ = 90
Symmetry Space Group P 21 3
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 RAYONIX MX225HE 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 3 19.1 99.2 0.093 18.7 4.8 23931
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 3 3.05 99.1 0.57 3 4.7
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 1oe1 3 19.1 22698 1217 98.79 0.17453 0.17135 0.1773 0.23279 0.2324 RANDOM 53.345
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.607 r_dihedral_angle_4_deg 22.273 r_dihedral_angle_3_deg 17.87 r_dihedral_angle_1_deg 7.892 r_long_range_B_refined 7.241 r_long_range_B_other 7.241 r_mcangle_other 5.183 r_mcangle_it 5.182 r_scangle_other 5.111 r_mcbond_it 3.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.607 r_dihedral_angle_4_deg 22.273 r_dihedral_angle_3_deg 17.87 r_dihedral_angle_1_deg 7.892 r_long_range_B_refined 7.241 r_long_range_B_other 7.241 r_mcangle_other 5.183 r_mcangle_it 5.182 r_scangle_other 5.111 r_mcbond_it 3.283 r_mcbond_other 3.281 r_scbond_it 3.209 r_scbond_other 3.209 r_angle_refined_deg 1.569 r_angle_other_deg 0.817 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6050 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing