☰ Navigation Tabs
The X-ray Crystal Structure of Molybdopterin Synthase from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FM0 PDB ENTRY 1FM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 295 2.0 M Sodium Formate, 0.1 M Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.922 α = 90 b = 45.754 β = 93.36 c = 41.772 γ = 90
Symmetry Space Group C 1 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 100 CCD ADSC QUANTUM 4 2004-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
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 50 94.8 0.033 29 3.3 16442
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 2.07 71.4 0.065 2.1
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 1FM0 2 30 15548 824 94.95 0.15087 0.14866 0.1634 0.19321 0.2015 RANDOM 24.645
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] -1.02 0.23 2.02 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.473 r_dihedral_angle_4_deg 22.417 r_dihedral_angle_3_deg 13.586 r_dihedral_angle_1_deg 6.771 r_scangle_it 3.638 r_scbond_it 2.598 r_angle_refined_deg 1.551 r_mcangle_it 1.308 r_mcbond_it 1.162 r_angle_other_deg 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.473 r_dihedral_angle_4_deg 22.417 r_dihedral_angle_3_deg 13.586 r_dihedral_angle_1_deg 6.771 r_scangle_it 3.638 r_scbond_it 2.598 r_angle_refined_deg 1.551 r_mcangle_it 1.308 r_mcbond_it 1.162 r_angle_other_deg 0.83 r_symmetry_hbond_refined 0.275 r_symmetry_vdw_refined 0.262 r_mcbond_other 0.252 r_nbd_refined 0.217 r_symmetry_vdw_other 0.192 r_xyhbond_nbd_refined 0.185 r_nbd_other 0.183 r_nbtor_refined 0.181 r_chiral_restr 0.103 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1761 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection MOLREP phasing