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Crystal structure analysis of PDZ domain B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 25% PEG3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.141 α = 90 b = 26.867 β = 112.12 c = 42.789 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 Bruker DIP-6040 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.65 SPring-8 BL44XU
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 0.98 21.47 99.4 0.044 17.1 3.7 42333 7.3
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) 0.98 1.03 99 0.446 2.9 3.7
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 0.98 20.75 40180 2140 99.38 0.15135 0.14977 0.1493 0.18043 0.1809 RANDOM 13.227
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] -0.07 0.13 -0.22 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.159 r_sphericity_free 12.093 r_dihedral_angle_3_deg 10.347 r_dihedral_angle_4_deg 8.869 r_sphericity_bonded 7.083 r_scangle_it 6.506 r_dihedral_angle_1_deg 5.922 r_scbond_it 4.864 r_mcangle_it 3.564 r_rigid_bond_restr 2.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.159 r_sphericity_free 12.093 r_dihedral_angle_3_deg 10.347 r_dihedral_angle_4_deg 8.869 r_sphericity_bonded 7.083 r_scangle_it 6.506 r_dihedral_angle_1_deg 5.922 r_scbond_it 4.864 r_mcangle_it 3.564 r_rigid_bond_restr 2.775 r_mcbond_it 2.493 r_angle_refined_deg 2.142 r_chiral_restr 0.136 r_bond_refined_d 0.023 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 733 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SCALA data scaling SHELXCD phasing SHELXE model building