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Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F8B PDB ENTRY 4F8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 293.15 16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride, VAPOR DIFFUSION, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.048 α = 90 b = 93.048 β = 90 c = 193.651 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 2011-02-11 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 2.498 22.151 91.6 0.14 6.8 4 34498 31577 46.6
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 2.498 2.54 88.8 0.65 2.3 3.9 1498
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4F8B 2.498 22.15 34397 29866 1592 91.46 0.23225 0.22836 0.2329 0.30485 0.2981 RANDOM 39.309
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.833 r_dihedral_angle_4_deg 11.448 r_dihedral_angle_3_deg 11.073 r_scangle_it 3.033 r_dihedral_angle_1_deg 2.322 r_angle_refined_deg 1.997 r_scbond_it 1.856 r_mcangle_it 1.424 r_mcbond_it 0.744 r_chiral_restr 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.833 r_dihedral_angle_4_deg 11.448 r_dihedral_angle_3_deg 11.073 r_scangle_it 3.033 r_dihedral_angle_1_deg 2.322 r_angle_refined_deg 1.997 r_scbond_it 1.856 r_mcangle_it 1.424 r_mcbond_it 0.744 r_chiral_restr 0.046 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6007 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 84
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing