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Crystal structure of L-aspartate/glutamate specific racemase in complex with L-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.3 M ammonium nitrate, 14~16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.53 α = 90 b = 81.25 β = 111.39 c = 83.96 γ = 90
Symmetry Space Group P 1 21 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 270 2015-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.987 PAL/PLS 7A (6B, 6C1)
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 50 98.3 6 3.3 56118
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 2 2.11 94.9 0.21 2.9 3.1
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 5ELL 2 29.32 53262 2833 98.1 0.17644 0.17328 0.1825 0.2363 0.2412 RANDOM 21.241
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_4_deg 20.234 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.877 r_long_range_B_refined 6.646 r_long_range_B_other 6.646 r_scangle_other 3.709 r_mcangle_other 2.754 r_mcangle_it 2.753 r_scbond_it 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_4_deg 20.234 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.877 r_long_range_B_refined 6.646 r_long_range_B_other 6.646 r_scangle_other 3.709 r_mcangle_other 2.754 r_mcangle_it 2.753 r_scbond_it 2.326 r_scbond_other 2.326 r_mcbond_it 1.804 r_mcbond_other 1.798 r_angle_refined_deg 1.738 r_angle_other_deg 0.903 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7274 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing