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CPS1 bound to allosteric inhibitor H3B-193
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 CPS1 protein was buffer exchanged into 50 mM glycyl-glycine pH 7.4, 50 mM KCl, 5% glycerol. CPS1 was concentrated to 10 mg/ml and H3B-4193 was added to a 5x excess molar ratio along with 1mM AMPPNP and 1mM NAG. Ligand bound complex crystals grew by hanging drop vapor diffusion in 20% PEG 3350 and 0.2M trisodium citrate
Crystal Properties Matthews coefficient Solvent content 3.12 60.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.587 α = 90 b = 132.342 β = 102.57 c = 142.443 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 120 PIXEL DECTRIS PILATUS3 6M 2019-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.00 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 139.03 99.3 0.098 0.11 0.048 6.2 5 281085
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 1.9 1.93 99.7 0.987 1.11 0.499 0.611 4.8
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 5DOT 1.9 139.03 268563 14084 99.92 0.1739 0.172 0.1811 0.2086 0.2156 RANDOM 30.467
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.349 r_dihedral_angle_4_deg 21.005 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.841 r_angle_other_deg 1.067 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.349 r_dihedral_angle_4_deg 21.005 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.841 r_angle_other_deg 1.067 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20622 Nucleic Acid Atoms Solvent Atoms 1623 Heterogen Atoms 56
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing