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Crystal structure of mouse prion protein complexed with Chlorpromazine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H88 PDB ENTRY 4H88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.78 55.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.262 α = 90 b = 106.883 β = 95.32 c = 75.594 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r 2012-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.007 APS 19-ID
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 2.2 50 97.3 0.08 14 3.5 32491 -3
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 2.2 2.28 86.4 0.57 1.5 2.2
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 PDB ENTRY 4H88 2.2 34.99 30848 1634 97.22 0.19664 0.19458 0.1974 0.23585 0.2409 RANDOM 60.404
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] -0.22 -0.46 1.8 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 23.948 r_dihedral_angle_3_deg 16.753 r_long_range_B_refined 7.674 r_long_range_B_other 7.418 r_dihedral_angle_1_deg 6.036 r_scangle_other 3.666 r_mcangle_other 3.297 r_scbond_other 2.302 r_mcangle_it 2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 23.948 r_dihedral_angle_3_deg 16.753 r_long_range_B_refined 7.674 r_long_range_B_other 7.418 r_dihedral_angle_1_deg 6.036 r_scangle_other 3.666 r_mcangle_other 3.297 r_scbond_other 2.302 r_mcangle_it 2.097 r_scbond_it 1.538 r_mcbond_it 1.327 r_mcbond_other 1.326 r_angle_refined_deg 1.322 r_angle_other_deg 0.834 r_chiral_restr 0.098 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 4184 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 21
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling