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Crystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDY PDB ENTRY 1YDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 O.1M HEPES PH 7.5, 25% PEG 3350, 0.2M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.19 61.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.312 α = 90 b = 183.546 β = 90 c = 176.79 γ = 90
Symmetry Space Group C 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 MAR CCD 165 mm MIRRORS 2006-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97940 APS 31-ID
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 2.2 50 97.1 0.058 0.054 8 5.7 124065 124065 47.63
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 2.2 2.28 97.1 0.32 0.36 1.8 4.5 12275
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 1YDY 2.2 20 120201 120201 3742 97.16 0.2362 0.23484 0.231 0.28044 0.2769 RANDOM 56.26
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] -1.89 1.05 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.272 r_dihedral_angle_3_deg 18.704 r_dihedral_angle_4_deg 16.105 r_scangle_it 14.218 r_scbond_it 11.081 r_dihedral_angle_1_deg 10.814 r_mcangle_it 9.072 r_mcbond_it 7.139 r_angle_refined_deg 1.133 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.272 r_dihedral_angle_3_deg 18.704 r_dihedral_angle_4_deg 16.105 r_scangle_it 14.218 r_scbond_it 11.081 r_dihedral_angle_1_deg 10.814 r_mcangle_it 9.072 r_mcbond_it 7.139 r_angle_refined_deg 1.133 r_nbtor_refined 0.292 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.162 r_nbd_refined 0.137 r_symmetry_vdw_refined 0.132 r_metal_ion_refined 0.014 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13120 Nucleic Acid Atoms Solvent Atoms 891 Heterogen Atoms 270
Software Software Software Name Purpose PHASER phasing MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling