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Crystal structure of the first PDZ domain of PREX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 1.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate, pH 6.2, vapor diffusion, sitting drop, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 5.6 293 1.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Soaked for 6 hours in 0.01 M potassium hexaiodoplatin-(IV)-ate and mother liquor, pH 5.6, vapor diffusion, sitting drop, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.135 α = 90 b = 78.135 β = 90 c = 54.691 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE RIGAKU RAXIS 2011-01-11 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU SATURN A200 2011-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418 2 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 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 2.27 25 100 0.075 15.1 10.4 8971
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) 2.27 2.35 100 0.674 10.4 870
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.285 20 8903 422 98.944 0.244 0.2424 0.2351 0.2691 0.2665 RANDOM 33.465
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] 1.279 0.64 1.279 -1.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_4_deg 11.913 r_dihedral_angle_1_deg 5.716 r_scangle_it 3.177 r_scbond_it 1.793 r_mcangle_it 1.307 r_angle_refined_deg 1.19 r_angle_other_deg 0.81 r_mcbond_it 0.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_4_deg 11.913 r_dihedral_angle_1_deg 5.716 r_scangle_it 3.177 r_scbond_it 1.793 r_mcangle_it 1.307 r_angle_refined_deg 1.19 r_angle_other_deg 0.81 r_mcbond_it 0.661 r_mcbond_other 0.099 r_chiral_restr 0.072 r_bond_refined_d 0.013 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 781 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling