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Crystal structure of cyclophilin ABH-like domain of human peptidylprolyl isomerase E isoform 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIT PDB entry 2BIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 34% PEG 8000, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.635 α = 90 b = 66.635 β = 90 c = 77.351 γ = 90
Symmetry Space Group P 42 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 IMAGE PLATE RIGAKU RAXIS HTC MIRRORS 2005-04-12 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 1.61 40 97.3 0.041 34.34 22683 -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) 1.61 1.67 81.4 0.16 6.36 2.2
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 2BIT 1.61 33.4 21499 1157 97.4 0.164 0.162 0.1719 0.196 0.2047 RANDOM 25.17
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] -0.34 -0.34 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_3_deg 11.079 r_dihedral_angle_4_deg 8.991 r_dihedral_angle_1_deg 5.795 r_rigid_bond_restr 3.934 r_scangle_it 3.86 r_scbond_it 3.72 r_sphericity_free 3.529 r_sphericity_bonded 2.728 r_mcangle_it 1.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_3_deg 11.079 r_dihedral_angle_4_deg 8.991 r_dihedral_angle_1_deg 5.795 r_rigid_bond_restr 3.934 r_scangle_it 3.86 r_scbond_it 3.72 r_sphericity_free 3.529 r_sphericity_bonded 2.728 r_mcangle_it 1.599 r_angle_refined_deg 1.197 r_mcbond_it 1.12 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.188 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 1265 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling