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Crystal structure of mouse prion protein complexed with Promazine
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 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.211 α = 90 b = 106.038 β = 95.68 c = 75.733 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 MARMOSAIC 325 mm CCD 2011-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 1.9 50 98.3 0.09 15.4 4.1 52155 -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 1.9 1.97 85.1 0.62 2 3.2
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 1.97 34.88 43247 2298 97.86 0.21741 0.21578 0.2186 0.24687 0.2465 RANDOM 40.636
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] -0.17 0.34 0.08 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.034 r_dihedral_angle_4_deg 18.827 r_dihedral_angle_3_deg 13.453 r_dihedral_angle_1_deg 6.014 r_long_range_B_refined 5.306 r_long_range_B_other 4.829 r_scangle_other 2.308 r_mcangle_it 2.031 r_mcangle_other 2.016 r_scbond_other 1.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.034 r_dihedral_angle_4_deg 18.827 r_dihedral_angle_3_deg 13.453 r_dihedral_angle_1_deg 6.014 r_long_range_B_refined 5.306 r_long_range_B_other 4.829 r_scangle_other 2.308 r_mcangle_it 2.031 r_mcangle_other 2.016 r_scbond_other 1.409 r_scbond_it 1.399 r_mcbond_it 1.212 r_mcbond_other 1.212 r_angle_refined_deg 1.082 r_angle_other_deg 0.786 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 4196 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling