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The structure of CaPGI in complex with fragments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 21 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.49 50.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.39 α = 90 b = 101.46 β = 90 c = 138.78 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 XE 16M 2022-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.5 69.39 82.8 1 18.9 10.2 163038
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.649
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 1.5 69.39 154831 8114 82.74 0.17956 0.1782 0.1881 0.20512 0.2118 RANDOM 16.878
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] -1.05 -0.3 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.186 r_dihedral_angle_1_deg 6.393 r_dihedral_angle_2_deg 6.235 r_long_range_B_refined 4.046 r_long_range_B_other 3.832 r_scangle_other 2.852 r_scbond_it 1.925 r_scbond_other 1.925 r_mcangle_other 1.59 r_mcangle_it 1.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.186 r_dihedral_angle_1_deg 6.393 r_dihedral_angle_2_deg 6.235 r_long_range_B_refined 4.046 r_long_range_B_other 3.832 r_scangle_other 2.852 r_scbond_it 1.925 r_scbond_other 1.925 r_mcangle_other 1.59 r_mcangle_it 1.589 r_angle_refined_deg 1.391 r_mcbond_it 1.116 r_mcbond_other 1.115 r_angle_other_deg 0.641 r_chiral_restr 0.099 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.002 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 8587 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling MOLREP phasing