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Crystal Structure of the cyclophiln_RING domain of human peptidylprolyl isomerase (cyclophilin)-like 2 isoform b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IIP PDB ENTRY 1IIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 0.8M Potassium Sodium Tartrate tetrahydrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.48 49.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.028 α = 90 b = 65.028 β = 90 c = 201.79 γ = 120
Symmetry Space Group P 31 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++ 2005-04-16 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 30 94.4 0.055 31.86 5.6 57395 -3
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) 1.65 1.71 63.2 0.479 1.72 1.7
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 1IIP 1.65 25.97 54423 2907 94.53 0.15775 0.15583 0.1633 0.19376 0.2005 RANDOM 27.17
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] 0.12 0.06 0.12 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.512 r_dihedral_angle_4_deg 14.919 r_dihedral_angle_3_deg 11.288 r_dihedral_angle_1_deg 5.686 r_scangle_it 4.931 r_scbond_it 4.427 r_sphericity_free 4.278 r_rigid_bond_restr 3.495 r_sphericity_bonded 3.484 r_mcangle_it 2.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.512 r_dihedral_angle_4_deg 14.919 r_dihedral_angle_3_deg 11.288 r_dihedral_angle_1_deg 5.686 r_scangle_it 4.931 r_scbond_it 4.427 r_sphericity_free 4.278 r_rigid_bond_restr 3.495 r_sphericity_bonded 3.484 r_mcangle_it 2.713 r_mcbond_it 2.064 r_angle_refined_deg 1.333 r_nbtor_refined 0.309 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing