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X-ray structure of murine Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) in complex with inhibitor oxalate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FOH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 20% PEG 4000, 0.05M MgCl2, 0.1M MES pH5.5
Crystal Properties Matthews coefficient Solvent content 2 38.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.603 α = 90 b = 103.348 β = 90.21 c = 86.597 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 PILATUS3 2M 2018-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-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 2.7 44.38 91.2 0.171 0.203 0.108 0.985 4.2 3.43 15791 38
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 2.71 2.97 51.4 0.543 0.648 0.351 0.757 1.4 3.32
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6FOH 2.7 44.37 15119 756 62.4 0.1893 0.1869 0.1921 0.2344 0.237 RANDOM 31.973
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] 0.95 0.24 -1.66 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.405 r_dihedral_angle_3_deg 20.511 r_dihedral_angle_4_deg 16.774 r_dihedral_angle_1_deg 8.211 r_angle_refined_deg 1.499 r_angle_other_deg 1.182 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.405 r_dihedral_angle_3_deg 20.511 r_dihedral_angle_4_deg 16.774 r_dihedral_angle_1_deg 8.211 r_angle_refined_deg 1.499 r_angle_other_deg 1.182 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6704 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing