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Crystal structure of the catalytic domain of rat phosphodiesterase 10A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other homology model of PDE10a
Crystallization Crystal Properties Matthews coefficient Solvent content 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.622 α = 90 b = 120.622 β = 90 c = 82.143 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 IMAGE PLATE RIGAKU RAXIS IIC mirrors 2002-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.8 30 91.4 0.063 12.2 37865
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) 1.8 1.86 53.9 0.675 2236
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 homology model of PDE10a 1.8 30 37822 2905 91.58 0.227 0.224 0.228 0.273 0.2756 RANDOM 35.117
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] -2.27 -1.13 -2.27 3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.391 r_scangle_it 3.245 r_scbond_it 2.071 r_angle_refined_deg 1.476 r_mcangle_it 1.312 r_angle_other_deg 0.896 r_mcbond_it 0.742 r_symmetry_hbond_refined 0.254 r_nbd_other 0.245 r_xyhbond_nbd_refined 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.391 r_scangle_it 3.245 r_scbond_it 2.071 r_angle_refined_deg 1.476 r_mcangle_it 1.312 r_angle_other_deg 0.896 r_mcbond_it 0.742 r_symmetry_hbond_refined 0.254 r_nbd_other 0.245 r_xyhbond_nbd_refined 0.233 r_nbd_refined 0.231 r_symmetry_vdw_other 0.21 r_metal_ion_refined 0.162 r_symmetry_vdw_refined 0.129 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2491 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction