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Crystal structure of alanine racemase from D-cycloserine producing Streptomyces lavendulae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFT PDB entry 1SFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.98 α = 90 b = 63.38 β = 120.14 c = 85.95 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 298 IMAGE PLATE RIGAKU RAXIS mirrors 2003-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2 100 94 0.111 0.092 6.7 2.9 24889 24889 24.1
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 2.11 86.9 0.609 0.475 1.5 2.1 6953
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1SFT 2 30 1 2 24889 24532 1193 92.6 0.21 0.197 0.197 0.252 RANDOM 33
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 x_dihedral_angle_d 26.8 x_scangle_it 5.96 x_scbond_it 3.95 x_mcangle_it 3.61 x_mcbond_it 2.33 x_angle_deg 1.1 x_improper_angle_d 0.63 x_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2851 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 15
Software Software Software Name Purpose X-PLOR refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing