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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 napthylalanine
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 3.8 67.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.67 α = 90 b = 217.67 β = 90 c = 263.15 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 PIXEL 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 2.44 153.25 100 0.09 17.7 10.2 88697 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 2.44 2.5 100 0.71 3.4 10.4
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 2.44 107.89 84472 4220 99.99 0.17453 0.17222 0.1728 0.22052 0.2212 RANDOM 49.197
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] -0.49 -0.24 -0.49 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.266 r_dihedral_angle_4_deg 24.535 r_dihedral_angle_3_deg 18.234 r_mcangle_it 7.33 r_dihedral_angle_1_deg 7.195 r_scbond_it 6.513 r_mcbond_it 5.22 r_angle_refined_deg 2.241 r_chiral_restr 0.142 r_bond_refined_d 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.266 r_dihedral_angle_4_deg 24.535 r_dihedral_angle_3_deg 18.234 r_mcangle_it 7.33 r_dihedral_angle_1_deg 7.195 r_scbond_it 6.513 r_mcbond_it 5.22 r_angle_refined_deg 2.241 r_chiral_restr 0.142 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 10912 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing