☰ Navigation Tabs
AmiP amidase-3 from Thermus parvatiensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 0.1 M hepes pH 7.8, 65 % MPD
Crystal Properties Matthews coefficient Solvent content 2.45 49.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.539 α = 90 b = 97.988 β = 90 c = 148.723 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 PIXEL DECTRIS EIGER2 XE 16M 2019-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.2824 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.79 46.53 96.9 0.035 0.05 0.035 0.999 9.2 1.9 86433
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.83 69.3 1.132 1.601 1.132 0.283 0.8 1.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.793 43.679 86337 4282 96.825 0.187 0.1848 0.1865 0.2253 0.227 Random selection 38.893
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] -0.132 0.067 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.794 r_dihedral_angle_4_deg 17.401 r_dihedral_angle_3_deg 13.106 r_lrange_other 7.46 r_lrange_it 7.458 r_dihedral_angle_1_deg 6.103 r_scangle_it 5.89 r_scangle_other 5.814 r_mcangle_other 4.19 r_mcangle_it 4.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.794 r_dihedral_angle_4_deg 17.401 r_dihedral_angle_3_deg 13.106 r_lrange_other 7.46 r_lrange_it 7.458 r_dihedral_angle_1_deg 6.103 r_scangle_it 5.89 r_scangle_other 5.814 r_mcangle_other 4.19 r_mcangle_it 4.189 r_scbond_it 4.098 r_scbond_other 4.049 r_mcbond_it 3.195 r_mcbond_other 3.194 r_angle_refined_deg 1.604 r_angle_other_deg 1.393 r_nbd_refined 0.212 r_nbd_other 0.191 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_other 0.149 r_symmetry_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.108 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.073 r_metal_ion_refined 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6302 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling SHELXDE phasing xia2 data reduction AutoSol phasing autoSHARP phasing XDS data reduction Coot model building