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Crystal structure of D-threonine aldolase from Chlamydomonas reinhardtii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 PEG 1540, 2-methyl-2,4-pentanediol, Magnesium nitrate
Crystal Properties Matthews coefficient Solvent content 2.1 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.792 α = 77.07 b = 74.096 β = 69.34 c = 89.939 γ = 71.93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210r 2015-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 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 1.85 83.46 88.6 0.044 0.062 0.044 9.2 1.6 111548
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 1.85 1.95 91.3 0.142 0.142 0.201 0.142 5.4 1.6
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 4V15 1.85 83.46 105911 5566 88.5 0.2187 0.2171 0.2171 0.249 0.2491 RANDOM 25.556
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 r_dihedral_angle_2_deg 35.42 r_dihedral_angle_4_deg 18.246 r_dihedral_angle_3_deg 16.484 r_dihedral_angle_1_deg 6.246 r_angle_refined_deg 1.384 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11654 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing