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Crystal structure of PDE10A catalytic domain complexed with LHB-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1M Hepes (pH 7.5), 0.2M MgCl2, 18% PEG 3350, 50mM 2-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.12 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.151 α = 90 b = 81.328 β = 90 c = 158.207 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD OXFORD ONYX CCD 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 79.1 97.86 0.063 11.7 4.6 15928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 0.209
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 1OUP 2.8 79.1 15129 776 97.66 0.23798 0.23435 0.2379 0.30662 0.3044 RANDOM 33.328
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] 0.04 0.06 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.255 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 15.184 r_dihedral_angle_1_deg 5.757 r_long_range_B_refined 3.76 r_long_range_B_other 3.759 r_mcangle_it 1.934 r_mcangle_other 1.934 r_scangle_other 1.242 r_angle_refined_deg 1.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.255 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 15.184 r_dihedral_angle_1_deg 5.757 r_long_range_B_refined 3.76 r_long_range_B_other 3.759 r_mcangle_it 1.934 r_mcangle_other 1.934 r_scangle_other 1.242 r_angle_refined_deg 1.175 r_mcbond_it 1.097 r_mcbond_other 1.095 r_angle_other_deg 0.929 r_scbond_it 0.701 r_scbond_other 0.7 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5003 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing