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Structure of aminoacid racemase in complex with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 2-propanol, Mg acetate, cacodylate
Crystal Properties Matthews coefficient Solvent content 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.027 α = 90 b = 169.017 β = 90 c = 178.009 γ = 90
Symmetry Space Group P 21 21 21
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 270 2013-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.94 50 99.7 0.111 15.6 6.7 132236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.97 99.9 0.293 6.4 6572
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 2EO5 1.94 50 125133 6650 99.36 0.1494 0.1474 0.1502 0.1875 0.1879 RANDOM 21.97
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] 1.33 -0.44 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_dihedral_angle_4_deg 15.722 r_dihedral_angle_3_deg 12.466 r_dihedral_angle_1_deg 6.215 r_mcangle_it 2.377 r_angle_refined_deg 1.836 r_mcbond_it 1.825 r_mcbond_other 1.825 r_angle_other_deg 0.958 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_dihedral_angle_4_deg 15.722 r_dihedral_angle_3_deg 12.466 r_dihedral_angle_1_deg 6.215 r_mcangle_it 2.377 r_angle_refined_deg 1.836 r_mcbond_it 1.825 r_mcbond_other 1.825 r_angle_other_deg 0.958 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13763 Nucleic Acid Atoms Solvent Atoms 1359 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data processing Coot model building