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Crystal structure of the peptidyl-prolyl isomerase (PPIase) from E. faecium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M Sodium acetate trihydrate pH 4.6, 0.1 M Cadmium chloride hydrate, 30% v/v Polyethylene glycol 400.
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.486 α = 90 b = 69.674 β = 102.81 c = 87.413 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 4M 2024-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 2.479 65.81 86.7 0.823 5.1 2.8 17572
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 2.479 7.958 0.02
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 2.48 65.81 16697 872 62.12 0.20916 0.20691 0.206 0.2501 0.2505 RANDOM 46.424
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] 0.64 -0.21 0.78 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.888 r_dihedral_angle_2_deg 9.031 r_long_range_B_refined 8.687 r_dihedral_angle_1_deg 6.591 r_mcangle_it 4.594 r_scbond_it 3.293 r_mcbond_it 2.659 r_angle_refined_deg 1.928 r_chiral_restr 0.132 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.888 r_dihedral_angle_2_deg 9.031 r_long_range_B_refined 8.687 r_dihedral_angle_1_deg 6.591 r_mcangle_it 4.594 r_scbond_it 3.293 r_mcbond_it 2.659 r_angle_refined_deg 1.928 r_chiral_restr 0.132 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4189 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing AutoProcess data scaling