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Crystal structure of D-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VFH PDB entry 1VFH
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 298.0K
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.96 α = 90 b = 63.55 β = 118.61 c = 84.62 γ = 90
Symmetry Space Group P 1 21 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 2003-09-06 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 1.9 100 99.7 0.128 0.109 5 3.6 60275 60275 17.1
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) 1.9 2 99.1 0.532 0.454 2.2 3.6 8688
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 (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 1VFH 1.9 30 1 2 59784 3008 97.8 0.23 0.209 0.209 0.265 RANDOM 26.1
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 5.86 x_scbond_it 3.99 x_mcangle_it 3.44 x_mcbond_it 2.41 x_angle_deg 1.2 x_improper_angle_d 0.65 x_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5712 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 45
Software Software Software Name Purpose X-PLOR refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing