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Crystal structure of cyclophilin from Leishmania donovani ligated with cyclosporin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HAQ PDB ENTRY 2HAQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.02M TRIS, 15% PEG3350, 0.1M NACL, 0.02% AZIDE, PH 8.5, 6% ETHYL ALCOHOL, CONCENTRATION: 10 MG/ML 1:1 CYCLOPHILIN-CYCLOSPORIN COMPLEX, TEMPERATURE 292K, BATCH METHOD, PH 8.50, SMALL TUBES
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.81 α = 90 b = 83.125 β = 103.03 c = 73.58 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 293 IMAGE PLATE MAR scanner 300 mm plate OSMIC MAXFLUX CONFOCAL MULTILAY 2008-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.6 30 95.3 0.052 14.1 4.11 12040 2 52.4
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 2.6 2.69 96.5 0.251 2.6 5.3
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 2HAQ 2.6 27.48 12040 623 95.1 0.207 0.207 0.2082 0.251 0.2536 RANDOM 49.6
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] 12.41 1.4 2.4 -14.81
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_angle_deg 1.4 c_improper_angle_d 0.78 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_angle_deg 1.4 c_improper_angle_d 0.78 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2728 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling