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Crystal structure of amidase from Pseudonocardia acaciae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG8000, NaCl, CAPS, pH 10.5.
Crystal Properties Matthews coefficient Solvent content 2.76 55.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.28 α = 90 b = 165.28 β = 90 c = 160.612 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 4M 2022-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.04 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3 44.119 99.8 0.992 11.9 14.4 42219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 0.727
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.02 44.119 42214 1940 99.757 0.204 0.2018 0.2072 0.2587 0.2611 55.92
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] 0.853 0.853 -1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.921 r_dihedral_angle_6_deg 15.044 r_lrange_other 8.723 r_lrange_it 8.722 r_dihedral_angle_1_deg 5.892 r_scangle_it 5.342 r_scangle_other 5.341 r_mcangle_it 5.164 r_mcangle_other 5.164 r_dihedral_angle_2_deg 4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.921 r_dihedral_angle_6_deg 15.044 r_lrange_other 8.723 r_lrange_it 8.722 r_dihedral_angle_1_deg 5.892 r_scangle_it 5.342 r_scangle_other 5.341 r_mcangle_it 5.164 r_mcangle_other 5.164 r_dihedral_angle_2_deg 4.11 r_mcbond_it 3.191 r_mcbond_other 3.191 r_scbond_it 3.18 r_scbond_other 3.18 r_angle_refined_deg 1.194 r_angle_other_deg 0.453 r_symmetry_xyhbond_nbd_refined 0.374 r_symmetry_nbd_other 0.227 r_nbd_other 0.222 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.215 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_other 0.129 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.061 r_chiral_restr 0.057 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13545 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing