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The crystal structure of a putative aminohydrolase from methicillin resistant Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YSJ PDB ENTRY 1YSJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 0.2M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 30.0% PEG 400, Microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.65 66.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.62 α = 115.4 b = 120.11 β = 94.64 c = 132.41 γ = 96.55
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 MARMOSAIC 225 mm CCD MIRRORS 2011-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9762 ESRF BM14
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 2.1 40.09 93.8 0.111 0.067 7.5 3.5 133741 2 26.34
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 2.1 2.21 88.6 0.404 0.253 2.9 3.2
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 1YSJ 2.1 39.32 127008 6731 93.8 0.2 0.199 0.2407 0.229 0.2642 RANDOM 38.361
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] -0.19 1.38 0.74 1.95 1.88 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.907 r_dihedral_angle_3_deg 16.687 r_dihedral_angle_4_deg 15.905 r_dihedral_angle_1_deg 5.752 r_scangle_it 2.699 r_scbond_it 1.606 r_angle_refined_deg 1.205 r_mcangle_it 0.88 r_mcbond_it 0.454 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.907 r_dihedral_angle_3_deg 16.687 r_dihedral_angle_4_deg 15.905 r_dihedral_angle_1_deg 5.752 r_scangle_it 2.699 r_scbond_it 1.606 r_angle_refined_deg 1.205 r_mcangle_it 0.88 r_mcbond_it 0.454 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 11751 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 81
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling