☰ Navigation Tabs
Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BP1 PDB ENTRY 3BP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293.15 16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride or magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.507 α = 90 b = 93.507 β = 90 c = 193.696 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315r mirrors 2006-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 1.000003 SSRL BL9-1
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 2.502 41.56 98.7 0.102 7.8 9.9 34623 34623 1 1 54.7
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 2.502 2.57 89.9 0.29 2.1 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3BP1 2.502 41.56 33897 32475 1720 98.72 0.19334 0.18918 0.1983 0.27195 0.2677 RANDOM 42.536
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] 1.93 0.96 1.93 -2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.639 r_dihedral_angle_3_deg 19.63 r_dihedral_angle_4_deg 19.121 r_dihedral_angle_1_deg 7.533 r_scangle_it 4.348 r_scbond_it 2.923 r_mcangle_it 2.21 r_angle_refined_deg 2.057 r_mcbond_it 1.339 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.639 r_dihedral_angle_3_deg 19.63 r_dihedral_angle_4_deg 19.121 r_dihedral_angle_1_deg 7.533 r_scangle_it 4.348 r_scbond_it 2.923 r_mcangle_it 2.21 r_angle_refined_deg 2.057 r_mcbond_it 1.339 r_nbtor_refined 0.329 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.251 r_metal_ion_refined 0.238 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.129 r_bond_refined_d 0.024 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6013 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 85
Software Software Software Name Purpose Blu-Ice data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling