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PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z104474062
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 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.595 α = 90 b = 99.614 β = 90 c = 127.835 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 2023-09-11 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 1.92 78.59 99.6 0.176 0.183 0.05 0.998 8.4 13.6 48653
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 1.92 1.96 97.8 1.076 1.117 0.3 0.938 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.92 78.58 44212 2253 95.01 0.3251 0.32277 0.37008 0.3004 RANDOM 53.211
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] 0.41 -0.03 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_4_deg 16.204 r_long_range_B_refined 7.475 r_long_range_B_other 7.446 r_dihedral_angle_1_deg 6.113 r_scangle_other 3.774 r_mcangle_it 3.663 r_mcangle_other 3.663 r_scbond_it 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_4_deg 16.204 r_long_range_B_refined 7.475 r_long_range_B_other 7.446 r_dihedral_angle_1_deg 6.113 r_scangle_other 3.774 r_mcangle_it 3.663 r_mcangle_other 3.663 r_scbond_it 1.71 r_scbond_other 1.705 r_mcbond_other 1.647 r_mcbond_it 1.631 r_angle_refined_deg 1.304 r_angle_other_deg 1.088 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 4302 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction