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PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z608061328
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 2.36 47.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.308 α = 90 b = 99.305 β = 90 c = 128.539 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 1.87 78.59 99.5 0.265 0.275 0.074 0.996 6.3 13.8 52262
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.91 92.6 12.737 3.394 0.355 13.8
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 1.87 78.59 48451 2433 96.89 0.26618 0.26338 0.2755 0.32045 0.3251 RANDOM 46.97
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] -0.76 -0.53 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.209 r_dihedral_angle_4_deg 19.26 r_dihedral_angle_3_deg 17.587 r_long_range_B_refined 16.092 r_long_range_B_other 15.83 r_dihedral_angle_1_deg 7.576 r_scangle_other 5.508 r_mcangle_it 5.002 r_mcangle_other 5.001 r_scbond_other 2.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.209 r_dihedral_angle_4_deg 19.26 r_dihedral_angle_3_deg 17.587 r_long_range_B_refined 16.092 r_long_range_B_other 15.83 r_dihedral_angle_1_deg 7.576 r_scangle_other 5.508 r_mcangle_it 5.002 r_mcangle_other 5.001 r_scbond_other 2.991 r_scbond_it 2.988 r_mcbond_other 2.689 r_mcbond_it 2.61 r_angle_refined_deg 1.572 r_angle_other_deg 1.2 r_chiral_restr 0.069 r_bond_refined_d 0.008 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 4287 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction