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CaPETaseM9 SEC loop of 9CL 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, 0.2M ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 1.93 36.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.099 α = 62.98 b = 74.498 β = 87.75 c = 80.189 γ = 80.06
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 1.63 50 95.9 0.99 6.42 3.1 101820
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 1.63 1.69 0.3223
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 1.63 28.14 95888 5047 95.1 0.185 0.18322 0.1938 0.21924 0.227 RANDOM 23.75
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] -0.26 -0.75 -0.51 0.98 -0.15 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.82 r_dihedral_angle_2_deg 8.797 r_dihedral_angle_1_deg 6.816 r_long_range_B_refined 5.383 r_long_range_B_other 5.365 r_scangle_other 4.119 r_mcangle_other 3.115 r_mcangle_it 3.114 r_scbond_it 2.803 r_scbond_other 2.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.82 r_dihedral_angle_2_deg 8.797 r_dihedral_angle_1_deg 6.816 r_long_range_B_refined 5.383 r_long_range_B_other 5.365 r_scangle_other 4.119 r_mcangle_other 3.115 r_mcangle_it 3.114 r_scbond_it 2.803 r_scbond_other 2.802 r_mcbond_it 2.168 r_mcbond_other 2.166 r_angle_refined_deg 1.698 r_angle_other_deg 0.608 r_chiral_restr 0.091 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 7768 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing