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Structure of the PDZ domain of human PDLIM7 bound to a C-terminal extension from human beta-tropomyosin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other homology based model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1M HEPES; 10% isopropanol; 20% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.052 α = 90 b = 55.404 β = 90 c = 57.316 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 MARMOSAIC 225 mm CCD 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9182 SLS X10SA
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 1.11 39.84 99.4 0.042 0.038 5.1 58681 58329
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) 1.11 1.15 100 0.144 0.121 11 4.6
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 homoly based model 1.11 39.84 58681 55322 2946 99.4 0.13272 0.13272 0.13143 0.132 0.15679 0.1563 RANDOM 7.247
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] -0.18 0.01 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.656 r_dihedral_angle_1_deg 26.903 r_dihedral_angle_4_deg 22.579 r_dihedral_angle_3_deg 10.618 r_sphericity_free 7.214 r_scangle_it 3.471 r_sphericity_bonded 3.269 r_scbond_it 2.667 r_mcangle_it 2.248 r_angle_refined_deg 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.656 r_dihedral_angle_1_deg 26.903 r_dihedral_angle_4_deg 22.579 r_dihedral_angle_3_deg 10.618 r_sphericity_free 7.214 r_scangle_it 3.471 r_sphericity_bonded 3.269 r_scbond_it 2.667 r_mcangle_it 2.248 r_angle_refined_deg 1.69 r_mcbond_it 1.622 r_angle_other_deg 1.465 r_rigid_bond_restr 1.211 r_mcbond_other 0.587 r_symmetry_vdw_other 0.279 r_nbd_refined 0.224 r_nbd_other 0.208 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.133 r_chiral_restr 0.113 r_nbtor_other 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1405 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing