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Crystal structure of the PDZ domain of MPP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.95 58.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.616 α = 90 b = 66.616 β = 90 c = 46.475 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2010-06-13 M SINGLE WAVELENGTH 1 1 x-ray 100 CCD ADSC QUANTUM 315 2010-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97904 APS 19-ID 2 ROTATING ANODE RIGAKU FR-E DW 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 2,1 1.3 40 99.8 0.041 14.6 5.6 28982
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) 1.3 1.32 100 0.751 5.5 2847
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.3 33.308 28929 1449 99.807 0.184 0.1839 0.1908 0.2063 RANDOM 12.991
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] 0.584 0.292 0.584 -0.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_3_deg 10.9 r_dihedral_angle_1_deg 6.733 r_dihedral_angle_4_deg 6.682 r_scangle_it 6.028 r_scbond_it 3.989 r_mcangle_it 2.973 r_mcbond_it 1.902 r_angle_refined_deg 1.679 r_rigid_bond_restr 1.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_3_deg 10.9 r_dihedral_angle_1_deg 6.733 r_dihedral_angle_4_deg 6.682 r_scangle_it 6.028 r_scbond_it 3.989 r_mcangle_it 2.973 r_mcbond_it 1.902 r_angle_refined_deg 1.679 r_rigid_bond_restr 1.413 r_angle_other_deg 0.921 r_mcbond_other 0.565 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 617 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction SHELXDE phasing