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Crystal Structure of PqqC Active Site Mutant Y175F in Complex with PQQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OTV PDB ENTRY 1OTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.607 α = 90 b = 116.775 β = 90 c = 68.279 γ = 90
Symmetry Space Group P 21 21 2
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 2008-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.3 37.7 88.4 0.188 0.173 10.5 6.5 124411
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.37 53.1 0.855 0.738 1.3 3 10702
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 PDB ENTRY 1OTV 1.3 37.7 124354 6232 88.24 0.165 0.164 0.1699 0.198 0.2018 RANDOM 12.088
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] -0.63 -0.71 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.688 r_dihedral_angle_4_deg 16.447 r_dihedral_angle_3_deg 13.102 r_sphericity_free 9.607 r_dihedral_angle_1_deg 5.758 r_scangle_it 4.361 r_sphericity_bonded 4.155 r_scbond_it 3.358 r_mcangle_it 2.376 r_mcbond_it 1.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.688 r_dihedral_angle_4_deg 16.447 r_dihedral_angle_3_deg 13.102 r_sphericity_free 9.607 r_dihedral_angle_1_deg 5.758 r_scangle_it 4.361 r_sphericity_bonded 4.155 r_scbond_it 3.358 r_mcangle_it 2.376 r_mcbond_it 1.897 r_angle_refined_deg 1.708 r_rigid_bond_restr 1.643 r_angle_other_deg 1.162 r_mcbond_other 0.824 r_symmetry_vdw_refined 0.603 r_symmetry_hbond_refined 0.494 r_symmetry_vdw_other 0.488 r_nbd_refined 0.242 r_nbd_other 0.211 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.11 r_nbtor_other 0.083 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4152 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 74
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction