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Staphylococcus aureus molybdopterin synthase in complex with precursor Z
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q5W PDB entry 2Q5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 18% PEG 8000, 0.1% polyvinylpyrrollidone K15, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.639 α = 90 b = 58.1 β = 90 c = 331.817 γ = 90
Symmetry Space Group P 2 2 21
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 315 2005-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.5 50 96.9 0.071 13.9 5.3 38004
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) 2.5 2.56 83.1 0.631 3.6 2132
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 2Q5W 2.5 30 37933 1900 96.77 0.209 0.207 0.2091 0.254 0.2616 RANDOM 57.947
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] 3.92 0.48 -4.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.903 r_dihedral_angle_3_deg 14.448 r_dihedral_angle_4_deg 12.962 r_dihedral_angle_1_deg 6.446 r_angle_refined_deg 1.077 r_scangle_it 0.961 r_angle_other_deg 0.708 r_scbond_it 0.6 r_mcangle_it 0.334 r_mcbond_it 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.903 r_dihedral_angle_3_deg 14.448 r_dihedral_angle_4_deg 12.962 r_dihedral_angle_1_deg 6.446 r_angle_refined_deg 1.077 r_scangle_it 0.961 r_angle_other_deg 0.708 r_scbond_it 0.6 r_mcangle_it 0.334 r_mcbond_it 0.27 r_nbd_refined 0.185 r_nbtor_refined 0.175 r_nbd_other 0.165 r_symmetry_vdw_other 0.163 r_xyhbond_nbd_refined 0.141 r_symmetry_vdw_refined 0.141 r_nbtor_other 0.078 r_chiral_restr 0.065 r_mcbond_other 0.048 r_symmetry_hbond_refined 0.04 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6997 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 92
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction