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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 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.31 α = 90 b = 101.44 β = 90 c = 139.13 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 1.7 59.76 99.3 0.998 8.7 11.4 135074
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 1.7 1.73 0.344
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 1.7 59.76 128132 6685 99.07 0.186 0.18422 0.1949 0.22063 0.2294 RANDOM 19.809
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] -0.25 -0.67 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.172 r_dihedral_angle_2_deg 7.94 r_dihedral_angle_1_deg 6.632 r_long_range_B_refined 4.745 r_long_range_B_other 4.618 r_scangle_other 3.914 r_scbond_it 2.626 r_scbond_other 2.625 r_mcangle_it 1.995 r_mcangle_other 1.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.172 r_dihedral_angle_2_deg 7.94 r_dihedral_angle_1_deg 6.632 r_long_range_B_refined 4.745 r_long_range_B_other 4.618 r_scangle_other 3.914 r_scbond_it 2.626 r_scbond_other 2.625 r_mcangle_it 1.995 r_mcangle_other 1.995 r_angle_refined_deg 1.485 r_mcbond_it 1.474 r_mcbond_other 1.474 r_angle_other_deg 0.615 r_chiral_restr 0.1 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 8604 Nucleic Acid Atoms Solvent Atoms 737 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling MOLREP phasing