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Crystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - L6T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 sodium citrate, HEPES-NaOH, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.64 α = 90 b = 65.64 β = 90 c = 184.07 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 PIXEL Bruker PHOTON II 2020-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.999 24.17 99.67 0.25 10.6 2.23 23492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.999 2.07 0.25
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 2.2 24.16 22393 1126 97.17 0.18617 0.18326 0.1952 0.24438 0.2483 RANDOM 16.614
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] 0.15 0.08 0.15 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.568 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 14.537 r_dihedral_angle_1_deg 7.061 r_long_range_B_refined 4.446 r_long_range_B_other 4.445 r_scangle_other 2.769 r_mcangle_it 1.92 r_mcangle_other 1.92 r_scbond_it 1.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.568 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 14.537 r_dihedral_angle_1_deg 7.061 r_long_range_B_refined 4.446 r_long_range_B_other 4.445 r_scangle_other 2.769 r_mcangle_it 1.92 r_mcangle_other 1.92 r_scbond_it 1.692 r_scbond_other 1.692 r_angle_refined_deg 1.498 r_angle_other_deg 1.273 r_mcbond_it 1.162 r_mcbond_other 1.161 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 3437 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHENIX phasing