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Structure of Pin1 WW Domain Sequence 3 with [R,R]-ACPC Loop Substitution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GWT PDB entry 4GWT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M Tris, pH 8.5, 3.0 M sodium chloride (Hampton Index #12), cryoprotection: dragged through Paratone-N prior to freezing
Crystal Properties Matthews coefficient Solvent content 2.83 56.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.173 α = 90 b = 48.173 β = 90 c = 37.214 γ = 90
Symmetry Space Group P 43 21 2
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 2014-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) 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 1.8 48.17 99.9 0.076 0.015 25.1 26.4 4398 31.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 1.902 0.36 2.3 28.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4GWT 1.8 34.06 3963 406 99.86 0.235 0.2307 0.2392 0.27491 0.2808 RANDOM 43.65
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] -0.17 -0.17 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.584 r_dihedral_angle_3_deg 15.701 r_dihedral_angle_4_deg 7.119 r_long_range_B_refined 7.05 r_long_range_B_other 6.9 r_dihedral_angle_1_deg 6.899 r_mcangle_other 2.769 r_mcangle_it 2.767 r_scangle_other 2.27 r_mcbond_it 1.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.584 r_dihedral_angle_3_deg 15.701 r_dihedral_angle_4_deg 7.119 r_long_range_B_refined 7.05 r_long_range_B_other 6.9 r_dihedral_angle_1_deg 6.899 r_mcangle_other 2.769 r_mcangle_it 2.767 r_scangle_other 2.27 r_mcbond_it 1.729 r_angle_refined_deg 1.71 r_mcbond_other 1.638 r_scbond_it 1.296 r_scbond_other 1.292 r_angle_other_deg 0.939 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 265 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing