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Crystal structure of Serine Racemase from Dictyostelium discoideum.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296 PEG 1540, sodium chloride, MPD, PIPES
Crystal Properties Matthews coefficient Solvent content 1.89 34.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.642 α = 87.4 b = 58.069 β = 72.75 c = 64.53 γ = 69.6
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 ADSC QUANTUM 315 2011-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.980 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.35 61.496 94.4 0.049 0.066 0.044 8.7 2.2 109316 109316
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 90.1 0.351 0.351 0.476 0.319 2.2 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1V71 1.35 36.75 103890 5411 94.42 0.2488 0.2478 0.2516 0.268 0.2584 RANDOM 19.954
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] 0.39 0.25 -0.64 -1.46 0.71 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.805 r_dihedral_angle_4_deg 20.058 r_dihedral_angle_3_deg 12.174 r_dihedral_angle_1_deg 5.592 r_angle_refined_deg 1.266 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4541 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing