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2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other search model found using BALBES software
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 7.6 mg/mL protein in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystals grew from 0.1 M MIB buffer pH 5.0, 25 % (w/v) PEG1500 (The PACT suite condition #14), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.11 41.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.735 α = 90 b = 118.31 β = 90 c = 129.008 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD Be-Lenses/Diamond Laue Mono 2010-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.37 30 99.6 0.077 18.36 4.9 30323 30323 -3
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) 2.37 2.41 100 0.572 2.66 4.9 1494
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 Balbes model 2.37 29.59 28741 28741 1533 99.52 0.20259 0.19972 0.2094 0.25683 0.2645 RANDOM 53.394
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] 1.52 -1.62 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.905 r_dihedral_angle_4_deg 14.623 r_dihedral_angle_3_deg 11.545 r_scangle_it 4.85 r_scbond_it 3.317 r_dihedral_angle_1_deg 3.007 r_mcangle_it 1.949 r_angle_refined_deg 1.567 r_mcbond_it 1.105 r_angle_other_deg 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.905 r_dihedral_angle_4_deg 14.623 r_dihedral_angle_3_deg 11.545 r_scangle_it 4.85 r_scbond_it 3.317 r_dihedral_angle_1_deg 3.007 r_mcangle_it 1.949 r_angle_refined_deg 1.567 r_mcbond_it 1.105 r_angle_other_deg 0.835 r_mcbond_other 0.299 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5866 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 24
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling