☰ Navigation Tabs
Structure of racemic Pin1 WW domain cocrystallized with DL-malic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IDH PDB ENTRY 2IDH, CORE BETA-SHEET FRAGMENT (RESI 260-263,268-272,277-279)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Peptide stock at 5 mg/mL (2.5 mg/mL L-peptide + 2.5 mg/L D-peptide), crystallized from 2.1 M DL-malic acid pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.985 α = 90 b = 65.985 β = 90 c = 38.599 γ = 90
Symmetry Space Group I 41/a
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD BRUKER SMART 6000 2011-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 33.32 100 0.069 22.85 13.3 4031 4031 41.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 100 0.29 9.1 190
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 PDB ENTRY 2IDH, CORE BETA-SHEET FRAGMENT (RESI 260-263,268-272,277-279) 2.25 33.32 4029 3857 172 99.97 0.2393 0.2394 0.2384 0.2375 0.2599 0.254 RANDOM 39.5828
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] -0.36 -0.36 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.884 r_dihedral_angle_4_deg 26.693 r_dihedral_angle_3_deg 18.687 r_dihedral_angle_1_deg 7.041 r_angle_refined_deg 1.495 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 276 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection HKL-2000 data reduction PHASER phasing