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Human Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP3) inhibitor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C02
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.73 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.932 α = 90 b = 72.932 β = 90 c = 382.728 γ = 90
Symmetry Space Group P 43 21 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 EIGER X 16M Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2024-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 37.45 96.7 0.209 0.111 0.968 5.4 4.3 28447 42.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 98.4 0.852 0.456 0.495 1.8 4.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 30.684 28419 1475 95.497 0.273 0.2702 0.2702 0.3333 0.3331 49.001
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] -3.18 -3.18 6.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.369 r_dihedral_angle_2_deg 12.745 r_dihedral_angle_6_deg 10.569 r_dihedral_angle_1_deg 6.777 r_lrange_it 4.679 r_mcangle_it 1.365 r_scangle_it 1.074 r_angle_refined_deg 1.062 r_mcbond_it 0.731 r_scbond_it 0.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.369 r_dihedral_angle_2_deg 12.745 r_dihedral_angle_6_deg 10.569 r_dihedral_angle_1_deg 6.777 r_lrange_it 4.679 r_mcangle_it 1.365 r_scangle_it 1.074 r_angle_refined_deg 1.062 r_mcbond_it 0.731 r_scbond_it 0.566 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.18 r_metal_ion_refined 0.121 r_chiral_restr 0.084 r_symmetry_xyhbond_nbd_refined 0.042 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6567 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 344
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing