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Crystal Structure of Modified Serine Racemase from S.pombe.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VE5 PDB ENTRY 1VE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 21% PEG4000, 0.2M Magnesium Acetate, 10% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.74 α = 90 b = 72.99 β = 102.41 c = 65.07 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 CCD MAR CCD 165 mm 2001-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.7 50 98.9 29883 29440 18.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 99.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB ENTRY 1VE5 1.7 9.96 2 29883 29360 2929 98.4 0.183 0.183 0.1828 0.209 0.2093 RANDOM 17.8
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] -1.13 0.5 0.04 1.09
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scbond_it 14.72 c_scangle_it 10.85 c_mcangle_it 1.6 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.76 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2433 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 22
Software Software Software Name Purpose CNS refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing