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Crystal Structure of Modified Serine Racemase complexed with Serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZPU PDB ENTRY 2ZPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 21% PEG 4000, 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 1.96 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.54 α = 90 b = 72.88 β = 101.73 c = 64.81 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 2002-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 SPring-8 BL44B2
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 2.2 99 99.2 13852 13720 13.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.26 94.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2ZPU 2.2 19.57 2 13645 1379 98.5 0.171 0.171 0.172 0.216 0.2205 RANDOM 23.5
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] -5.67 1.42 -0.18 5.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_scbond_it 17.21 c_scangle_it 13.92 c_mcangle_it 1.64 c_angle_deg 1.3 c_mcbond_it 1.11 c_improper_angle_d 0.77 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2433 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 29
Software Software Software Name Purpose CNS refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing