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Crystal structure of cyclophilin from Trypanosoma cruzi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DYW 1DYW.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 Ammonium Phosphate monobasic, Sodium Acetate, PEG8000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 25K, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.314 α = 109.55 b = 62.142 β = 104.21 c = 64.638 γ = 104.92
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 custom 2004-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0000 ALS 5.0.1
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 1.61 56.8 93.4 0.103 7.2 1.8 80854 80854 2 2
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 1.61 1.7 89.4 0.55 2 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1DYW.pdb 1.61 56.8 2 80854 80854 4251 93.4 0.179 0.18 0.17899 0.1898 0.19774 0.2096 RANDOM 15.335
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] -0.53 0.29 0.36 1.11 0.14 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.597 r_scangle_it 6.58 r_scbond_it 4.471 r_angle_other_deg 3.668 r_angle_refined_deg 2.61 r_mcangle_it 2.591 r_mcbond_it 1.637 r_symmetry_vdw_other 0.302 r_nbd_other 0.297 r_nbd_refined 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.597 r_scangle_it 6.58 r_scbond_it 4.471 r_angle_other_deg 3.668 r_angle_refined_deg 2.61 r_mcangle_it 2.591 r_mcbond_it 1.637 r_symmetry_vdw_other 0.302 r_nbd_other 0.297 r_nbd_refined 0.21 r_chiral_restr 0.189 r_symmetry_vdw_refined 0.177 r_nbtor_other 0.123 r_symmetry_hbond_refined 0.109 r_xyhbond_nbd_refined 0.094 r_bond_refined_d 0.038 r_gen_planes_other 0.022 r_gen_planes_refined 0.014 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5088 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ELVES data reduction ELVES data scaling EPMR phasing