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P411-PFA carbene transferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UCW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 mM ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.254 α = 90 b = 172.462 β = 90 c = 225.623 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1.87 50 91.8 0.056 21.6 2.4 147073
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 0.282 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5UCW 1.87 38.6 147073 7853 91.8 0.18882 0.18723 0.1949 0.21795 0.223 RANDOM 21.043
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] -0.42 0.42 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.698 r_dihedral_angle_4_deg 12.65 r_dihedral_angle_3_deg 11.953 r_dihedral_angle_1_deg 6.012 r_long_range_B_refined 3.177 r_long_range_B_other 3.022 r_mcangle_it 1.31 r_mcangle_other 1.31 r_scangle_other 1.247 r_angle_refined_deg 1.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.698 r_dihedral_angle_4_deg 12.65 r_dihedral_angle_3_deg 11.953 r_dihedral_angle_1_deg 6.012 r_long_range_B_refined 3.177 r_long_range_B_other 3.022 r_mcangle_it 1.31 r_mcangle_other 1.31 r_scangle_other 1.247 r_angle_refined_deg 1.216 r_angle_other_deg 1.132 r_mcbond_it 0.751 r_mcbond_other 0.751 r_scbond_it 0.732 r_scbond_other 0.732 r_chiral_restr 0.054 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.002 r_bond_other_d 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 14486 Nucleic Acid Atoms Solvent Atoms 985 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing