☰ Navigation Tabs
Crystal structure of copper nitrite reductase from Geobacillus kaustophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 0.1M Acetate, 5.5% PEG4000, 175mM ZnSO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.14 60.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.069 α = 90 b = 115.069 β = 90 c = 87.505 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 QUANTUM 210 2010-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.3 18.9 95.2 14.9 3.5 101119 101119 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 90.8 2.4 2.4
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 1kbw 1.3 18.9 96275 5038 95.09 0.1824 0.18162 0.1816 0.19747 0.1983 RANDOM 18.319
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] -1.05 -0.53 -1.05 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.177 r_dihedral_angle_3_deg 10.657 r_dihedral_angle_4_deg 8.663 r_dihedral_angle_1_deg 7.402 r_sphericity_free 3.516 r_sphericity_bonded 2.834 r_scangle_it 2.767 r_scbond_it 1.89 r_angle_refined_deg 1.296 r_mcangle_it 1.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.177 r_dihedral_angle_3_deg 10.657 r_dihedral_angle_4_deg 8.663 r_dihedral_angle_1_deg 7.402 r_sphericity_free 3.516 r_sphericity_bonded 2.834 r_scangle_it 2.767 r_scbond_it 1.89 r_angle_refined_deg 1.296 r_mcangle_it 1.175 r_rigid_bond_restr 0.925 r_mcbond_it 0.749 r_nbtor_refined 0.304 r_metal_ion_refined 0.266 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.192 r_symmetry_metal_ion_refined 0.167 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2350 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling