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CaPETaseM9 SEC loop of 10CL 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 15% (w/v) PEG 3350, 0.1 M Magnesium formate dihydrate
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.574 α = 118.73 b = 75.778 β = 95.89 c = 77.244 γ = 102.03
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 2023-11-29 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) 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 1.73 50 94.9 0.995 11.8 3.37 87626
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.79 0.153
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 1.73 25.83 83430 4392 95.19 0.18508 0.18303 0.1965 0.22458 0.2394 RANDOM 20.67
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] -0.02 -0.58 -1.12 -1.73 -0.82 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.197 r_dihedral_angle_2_deg 9.044 r_dihedral_angle_1_deg 6.908 r_long_range_B_refined 4.688 r_long_range_B_other 4.679 r_scangle_other 3.561 r_mcangle_it 2.538 r_mcangle_other 2.538 r_scbond_it 2.343 r_scbond_other 2.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.197 r_dihedral_angle_2_deg 9.044 r_dihedral_angle_1_deg 6.908 r_long_range_B_refined 4.688 r_long_range_B_other 4.679 r_scangle_other 3.561 r_mcangle_it 2.538 r_mcangle_other 2.538 r_scbond_it 2.343 r_scbond_other 2.343 r_mcbond_it 1.765 r_mcbond_other 1.765 r_angle_refined_deg 1.689 r_angle_other_deg 0.593 r_chiral_restr 0.086 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 7881 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing