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Molecular Analysis of the Interaction of the HDL Receptor SR-BI with the Adaptor Protein PDZK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 100mM Tris/HCl, 40% PEG 200, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.604 α = 90 b = 55.114 β = 90 c = 111.055 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 ADSC QUANTUM 210 mirrors 2009-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.1 NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.65 30.7 97.5 0.488 0.545 41.1 10.5 26518 26518 -3 26.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.65 1.86 91.7 0.055 0.056 3.7 5.8 1235
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2EDZ 1.8 29.91 19752 19752 1003 98.88 0.20158 0.20158 0.19973 0.2107 0.23763 0.2485 RANDOM 27.334
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] 0.02 0.11 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.405 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 15.274 r_dihedral_angle_1_deg 6.209 r_scangle_it 4.677 r_scbond_it 2.9 r_mcangle_it 1.887 r_angle_refined_deg 1.851 r_mcbond_it 1.1 r_angle_other_deg 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.405 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 15.274 r_dihedral_angle_1_deg 6.209 r_scangle_it 4.677 r_scbond_it 2.9 r_mcangle_it 1.887 r_angle_refined_deg 1.851 r_mcbond_it 1.1 r_angle_other_deg 0.967 r_mcbond_other 0.335 r_chiral_restr 0.123 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1666 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling