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Co-crystal structure of Human Protein-arginine deiminase type-4 (PAD4) with small molecule inhibitor JBI-589
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 299 0.1M HEPES pH 7.0, 5% (v/v) Tascimate pH 7.0, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.7 54.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.456 α = 90 b = 60.879 β = 104.585 c = 127.097 γ = 90
Symmetry Space Group I 1 2 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 EIGER X 16M 2022-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.88 46.81 99.6 0.05 0.999 19.6 7 18844
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 3.04 0.54 0.98
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4X8G 2.88 42.902 18829 940 99.372 0.209 0.2054 0.2091 0.2726 0.2687
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] -3.363 0.687 14.049 -9.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.287 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_4_deg 15.304 r_dihedral_angle_1_deg 7.514 r_lrange_it 6.919 r_lrange_other 6.918 r_mcangle_it 4.597 r_mcangle_other 4.597 r_scangle_it 4.245 r_scangle_other 4.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.287 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_4_deg 15.304 r_dihedral_angle_1_deg 7.514 r_lrange_it 6.919 r_lrange_other 6.918 r_mcangle_it 4.597 r_mcangle_other 4.597 r_scangle_it 4.245 r_scangle_other 4.245 r_mcbond_it 2.777 r_mcbond_other 2.775 r_scbond_it 2.549 r_scbond_other 2.549 r_angle_refined_deg 1.462 r_angle_other_deg 1.164 r_nbd_refined 0.22 r_nbd_other 0.204 r_symmetry_nbd_refined 0.19 r_symmetry_nbd_other 0.188 r_symmetry_xyhbond_nbd_other 0.178 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_nbtor_other 0.075 r_chiral_restr_other 0.058 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4429 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing