☰ Navigation Tabs
Crystal Structure of the peptidylprolyl isomerase domain of Human PPWD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 298 1.7M NH4SO4, 0.1M sodium cacodylate pH 5.7, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.658 α = 90 b = 39.893 β = 122.33 c = 115.638 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2005-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 1.65 23.2 91.4 0.036 34.86 3.4 59800 59800 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 63.1 2 2.6 4076
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 (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 1X07 1.65 23.2 59800 56773 3027 91.43 0.20169 0.19939 0.2056 0.24538 0.2498 RANDOM 46.339
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] -0.43 -1.5 1.67 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.094 r_dihedral_angle_4_deg 17.979 r_dihedral_angle_3_deg 12.934 r_sphericity_free 7.413 r_sphericity_bonded 5.758 r_dihedral_angle_1_deg 5.73 r_scangle_it 4.955 r_scbond_it 3.743 r_mcangle_it 3.318 r_mcbond_it 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.094 r_dihedral_angle_4_deg 17.979 r_dihedral_angle_3_deg 12.934 r_sphericity_free 7.413 r_sphericity_bonded 5.758 r_dihedral_angle_1_deg 5.73 r_scangle_it 4.955 r_scbond_it 3.743 r_mcangle_it 3.318 r_mcbond_it 2.54 r_rigid_bond_restr 2.25 r_angle_refined_deg 1.368 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3865 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing