☰ Navigation Tabs
Capra hircus reactive intermediate deaminase A mutant - A108D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1 M SPG, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.97 37.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.461 α = 90 b = 88.461 β = 90 c = 88.461 γ = 90
Symmetry Space Group P 21 3
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 EIGER R 4M 2021-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.968 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.57 44.27 100 0.048 0.05 1 41.08 41.2 62170 19.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.67 0.303 0.0267 0.99 10.78
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 FREE R-VALUE 1.57 44.27 32334 1563 99.636 0.144 0.1424 0.1433 0.1786 0.1772 25.116
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.391 r_lrange_it 15.559 r_lrange_other 14.408 r_dihedral_angle_3_deg 13.072 r_scangle_it 10.002 r_scangle_other 9.999 r_mcangle_other 9.157 r_mcangle_it 9.155 r_dihedral_angle_2_deg 8.456 r_scbond_it 6.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.391 r_lrange_it 15.559 r_lrange_other 14.408 r_dihedral_angle_3_deg 13.072 r_scangle_it 10.002 r_scangle_other 9.999 r_mcangle_other 9.157 r_mcangle_it 9.155 r_dihedral_angle_2_deg 8.456 r_scbond_it 6.706 r_scbond_other 6.703 r_mcbond_it 6.213 r_mcbond_other 6.181 r_dihedral_angle_1_deg 5.986 r_rigid_bond_restr 4.084 r_angle_refined_deg 1.682 r_angle_other_deg 0.568 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_other 0.203 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.173 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.13 r_ncsr_local_group_1 0.129 r_symmetry_nbd_refined 0.116 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1990 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MoRDa phasing