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Capra hircus reactive intermediate deaminase A mutant - R107W
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 8 298 0.1 M SPG, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.9 35.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.442 α = 90 b = 88.442 β = 90 c = 88.442 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 1.65 44.26 99.8 0.133 0.134 0.998 17.9 41.2 44033
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 1.74 1.77 0.785
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 NONE 1.654 44.26 27732 1451 99.741 0.166 0.1645 0.165 0.1917 0.1918 25.366
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 13.397 r_dihedral_angle_3_deg 10.201 r_dihedral_angle_2_deg 8.827 r_lrange_it 6.738 r_lrange_other 6.729 r_dihedral_angle_1_deg 6.007 r_scangle_it 5.359 r_scangle_other 5.358 r_scbond_it 3.782 r_scbond_other 3.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.397 r_dihedral_angle_3_deg 10.201 r_dihedral_angle_2_deg 8.827 r_lrange_it 6.738 r_lrange_other 6.729 r_dihedral_angle_1_deg 6.007 r_scangle_it 5.359 r_scangle_other 5.358 r_scbond_it 3.782 r_scbond_other 3.78 r_mcangle_other 3.474 r_mcangle_it 3.471 r_mcbond_it 2.377 r_mcbond_other 2.325 r_angle_refined_deg 1.237 r_angle_other_deg 0.432 r_nbd_refined 0.214 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.171 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_nbd_refined 0.129 r_ncsr_local_group_1 0.102 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1988 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MoRDa phasing