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Structure of ligand-bound mouse cGAMP hydrolase ENPP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 PEG 600, sodium acetate, magnesium acetate, polyvinylpyrrolidone
Crystal Properties Matthews coefficient Solvent content 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.35 α = 90 b = 102.35 β = 90 c = 172.891 γ = 120
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 S 6M 2017-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.2 88.638 91.8 0.16 0.204 0.124 5.4 2.1 30691 30691
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 90.6 0.723 0.723 0.927 0.573 0.8 2.1
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 4gtw 3.2 30.64 29094 1518 91.66 0.205 0.2014 0.2017 0.2733 0.2745 RANDOM 63.997
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] 1.25 0.63 1.25 -4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.002 r_dihedral_angle_4_deg 21.883 r_dihedral_angle_3_deg 18.987 r_dihedral_angle_1_deg 6.42 r_angle_refined_deg 1.405 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10682 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction PHASER phasing PDB_EXTRACT data extraction SCALA data scaling