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Cyclophilin from Trypanosoma cruzi bound to cyclosporin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XO7 1XO7, CYCLOPHILIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 50MM POTASSIUM PHOSPHATE, 40% PEG 8000, 2MM CYCLOSPORIN A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 25K, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.269 α = 110.49 b = 57.059 β = 108.21 c = 58.807 γ = 105.4
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 ADSC QUANTUM 4 2004-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.07 50 94.4 29952 1.8
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 2.07 2.12 94.2
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 1XO7, CYCLOPHILIN 2.07 49.39 29952 1590 94.4 0.172 0.169 0.1855 0.235 0.2502 RANDOM 25.08
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] -1.27 0.72 -0.62 1.16 -0.11 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.56 r_scangle_it 5.451 r_scbond_it 3.36 r_angle_refined_deg 2.056 r_mcangle_it 1.933 r_mcbond_it 1.093 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.56 r_scangle_it 5.451 r_scbond_it 3.36 r_angle_refined_deg 2.056 r_mcangle_it 1.933 r_mcbond_it 1.093 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.154 r_symmetry_hbond_refined 0.121 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4068 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms
Software Software Software Name Purpose EPMR phasing REFMAC refinement ELVES data reduction ELVES data scaling