☰ Navigation Tabs
Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase
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 5 277 PEG 4000, sodium acetate, ammonium acetate, glycerol
Crystal Properties Matthews coefficient Solvent content 2.06 40.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.181 α = 90 b = 80.708 β = 116.22 c = 87.991 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 ADSC QUANTUM 210r 2007-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.9 78.936 99.2 0.037 0.05 0.025 17.9 4 46230 46230
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 1.9 2 95.1 0.338 0.338 0.502 0.275 2.3 3.2
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 1.9 50.01 44006 2224 99.16 0.2075 0.2053 0.2087 0.2515 0.2536 RANDOM 36.781
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] -1.16 -0.19 4.03 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.618 r_dihedral_angle_4_deg 15.553 r_dihedral_angle_3_deg 14.672 r_dihedral_angle_1_deg 6.038 r_angle_refined_deg 1.374 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4963 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing