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PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z240654968
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 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.843 α = 90 b = 98.84 β = 90 c = 128.594 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 2023-10-09 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 1.85 78.38 100 0.213 0.221 0.06 0.997 7 13.7 54037
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 1.85 1.89 100 4.56 4.75 1.318 0.259 12.9
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 1.85 78.37 50480 2586 98.11 0.24855 0.24592 0.2531 0.29915 0.2836 RANDOM 49.509
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] -1.5 -1.09 2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_3_deg 16.76 r_long_range_B_refined 15.815 r_long_range_B_other 15.001 r_dihedral_angle_4_deg 13.861 r_dihedral_angle_1_deg 6.954 r_scangle_other 5.652 r_mcangle_it 4.634 r_mcangle_other 4.633 r_scbond_other 2.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_3_deg 16.76 r_long_range_B_refined 15.815 r_long_range_B_other 15.001 r_dihedral_angle_4_deg 13.861 r_dihedral_angle_1_deg 6.954 r_scangle_other 5.652 r_mcangle_it 4.634 r_mcangle_other 4.633 r_scbond_other 2.998 r_scbond_it 2.98 r_mcbond_other 2.544 r_mcbond_it 2.447 r_angle_refined_deg 1.486 r_angle_other_deg 1.192 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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 221 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction