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CaPETaseM9 + P289E variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG 3350, 0.04M Citricacid, 0.06 M BIS-TRIS propane pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.99 α = 90 b = 112.019 β = 90 c = 113.524 γ = 90
Symmetry Space Group P 21 21 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 EIGER2 S 9M 2024-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.22 50 93.5 0.113 0.12 0.037 0.993 16.2 7.4 145353
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.22 1.24 84.8 0.47 0.52 0.218 0.764 4.7
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 7YME 1.22 33.25 137968 7306 93.37 0.17606 0.17528 0.1789 0.19077 0.1939 RANDOM 12.121
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] 0.32 -0.07 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.629 r_dihedral_angle_2_deg 8.837 r_dihedral_angle_1_deg 6.57 r_long_range_B_refined 3.703 r_long_range_B_other 3.677 r_scangle_other 3.228 r_scbond_it 2.215 r_scbond_other 2.215 r_angle_refined_deg 1.965 r_mcangle_other 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.629 r_dihedral_angle_2_deg 8.837 r_dihedral_angle_1_deg 6.57 r_long_range_B_refined 3.703 r_long_range_B_other 3.677 r_scangle_other 3.228 r_scbond_it 2.215 r_scbond_other 2.215 r_angle_refined_deg 1.965 r_mcangle_other 1.82 r_mcangle_it 1.818 r_mcbond_it 1.257 r_mcbond_other 1.257 r_angle_other_deg 0.685 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3976 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction