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Crystal structure of Staphylococcus aureus hydrolase AmiA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LAT PDB ENTRY 3LAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1 M MES/imidazole, pH 6.5, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate, 0.02 M racemic sodium/potassium tartrate, 0.02 M sodium oxamate, 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% w/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.09 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.8 α = 90 b = 81.68 β = 128.84 c = 68.69 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 PIXEL DECTRIS PILATUS 2M-F 2011-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.12 48.164 92.4 21.1 6 158107 146370 -3 -3 13.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.15 59.7 1.8 2 6937
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 3LAT 1.124 40.84 1.99 158366 146365 7319 92.9 0.1218 0.1209 0.1208 0.1389 0.1382 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.207 f_angle_d 1.328 f_chiral_restr 0.084 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3285 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 41
Software Software Software Name Purpose RemDAq data collection PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling