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PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z1575337975
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.85 293 0.1M MES pH 6.85, 1.6M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.17 α = 90 b = 99.28 β = 90 c = 128.59 γ = 90
Symmetry Space Group I 2 2 2
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 9M 2023-09-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.97 49.64 96.4 0.222 0.231 0.063 0.997 8.6 13.4 43550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 100 4.545 4.715 1.246 0.301 14.2
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 1.97 49.69 41233 2118 95.94 0.24248 0.23923 0.2487 0.30422 0.2931 RANDOM 47.432
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] -0.37 -0.09 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.764 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 18.52 r_long_range_B_refined 8.679 r_long_range_B_other 8.669 r_dihedral_angle_1_deg 7.064 r_scangle_other 5.414 r_mcangle_it 4.647 r_mcangle_other 4.646 r_scbond_other 2.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.764 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 18.52 r_long_range_B_refined 8.679 r_long_range_B_other 8.669 r_dihedral_angle_1_deg 7.064 r_scangle_other 5.414 r_mcangle_it 4.647 r_mcangle_other 4.646 r_scbond_other 2.951 r_scbond_it 2.929 r_mcbond_other 2.605 r_mcbond_it 2.519 r_angle_refined_deg 1.514 r_angle_other_deg 1.187 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 4272 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction