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The structure of oxidised cyclophilin A from s. mansoni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZMF PDB ENTRY 1ZMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 2.5% GLYCEROL, 30% PEG5K MME, 2UM COPPER (II) SULPHATE, 0.1M SODIUM ACETATE PH 5.5
Crystal Properties Matthews coefficient Solvent content 1.82 31.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.203 α = 90 b = 59.249 β = 90 c = 61.474 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD MARRESEARCH 2006-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 1.8 40 98.8 0.07 19.6 8.9 227195 1
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 1.8 1.86 97.2 1.8 8.2
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 1ZMF 1.8 42.68 13196 696 98.7 0.183 0.182 0.1811 0.209 0.2089 RANDOM 13.31
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] 0.82 -0.43 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.655 r_dihedral_angle_4_deg 15.617 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 5.567 r_scangle_it 1.956 r_scbond_it 1.24 r_angle_refined_deg 1.13 r_mcangle_it 0.838 r_mcbond_it 0.537 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.655 r_dihedral_angle_4_deg 15.617 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 5.567 r_scangle_it 1.956 r_scbond_it 1.24 r_angle_refined_deg 1.13 r_mcangle_it 0.838 r_mcbond_it 0.537 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.197 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.111 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1271 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing