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L211Q, L254N, T262G mutant of carboxypeptidase T from Thermoactinomyces vulgaris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.4 SA
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.085 α = 90 b = 158.085 β = 90 c = 104.589 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 130 mm 2023-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.752680 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.96 30 99.97 0.11 0.115 5.8757 12.09 110357
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.07 99.99 0.36 0.376 2.05 9.41
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 (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 1.96 28.91 52826 2714 99.94 0.14649 0.14552 0.1591 0.1655 0.1757 RANDOM 14.85
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_2_deg 29.071 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 7.424 r_long_range_B_refined 5.219 r_long_range_B_other 4.748 r_scangle_other 3.43 r_scbond_it 2.387 r_scbond_other 2.286 r_mcangle_other 1.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.071 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 7.424 r_long_range_B_refined 5.219 r_long_range_B_other 4.748 r_scangle_other 3.43 r_scbond_it 2.387 r_scbond_other 2.286 r_mcangle_other 1.799 r_mcangle_it 1.788 r_angle_refined_deg 1.774 r_angle_other_deg 1.597 r_mcbond_it 1.328 r_mcbond_other 1.288 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2579 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing