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Crystal structure analysis of PDZ domain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 17% PEG2000mme, 85mM Tris-HCl, 8.5mM NiCl2, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.756 α = 90 b = 54.756 β = 90 c = 75.644 γ = 120
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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.9791 Photon Factory BL-5A
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 1.7 18.55 99 0.037 35.1 10.8 27607 26.2
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 1.7 1.79 93.9 0.376 4.2 7.8 3842
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.7 18.55 26202 1401 99.02 0.15075 0.14953 0.2115 0.1755 RANDOM 27.943
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] 5.31 5.31 -10.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.39 r_dihedral_angle_4_deg 16.845 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_1_deg 5.755 r_scangle_it 5.31 r_scbond_it 3.307 r_mcangle_it 2.143 r_angle_refined_deg 1.869 r_mcbond_it 1.264 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.39 r_dihedral_angle_4_deg 16.845 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_1_deg 5.755 r_scangle_it 5.31 r_scbond_it 3.307 r_mcangle_it 2.143 r_angle_refined_deg 1.869 r_mcbond_it 1.264 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2100 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction and data scaling SHELXCD phasing SHELXE model building