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N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A6G PDB ENTRY 4A6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 100 MM TRIS HCL PH 8.0; 15% (W/V) PEG 4K; 800 MM SODIUM FORMATE; PROTEIN AT 8 MG PER ML
Crystal Properties Matthews coefficient Solvent content 3.76 67.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.9 α = 90 b = 216.9 β = 90 c = 261.63 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS 6M 2014-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.52 107.35 100 0.1 17 10.2 79550 2
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 2.52 2.59 100 0.83 2.9 10
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 PDB ENTRY 4A6G 2.52 107.35 75765 3783 99.98 0.158 0.15635 0.1644 0.1902 0.1966 RANDOM 47.372
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] -1.04 -0.52 -1.04 3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.375 r_dihedral_angle_4_deg 21.936 r_dihedral_angle_3_deg 16.223 r_dihedral_angle_1_deg 6.025 r_scbond_it 5.326 r_mcangle_it 5.26 r_mcbond_it 3.785 r_mcbond_other 3.781 r_angle_refined_deg 1.809 r_angle_other_deg 1.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.375 r_dihedral_angle_4_deg 21.936 r_dihedral_angle_3_deg 16.223 r_dihedral_angle_1_deg 6.025 r_scbond_it 5.326 r_mcangle_it 5.26 r_mcbond_it 3.785 r_mcbond_other 3.781 r_angle_refined_deg 1.809 r_angle_other_deg 1.488 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.008 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10968 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing