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The structure of reduced 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 0.1M IMIDAZOLE/MALATE PH 5.5, 20 % PEG 600
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.654 α = 90 b = 59.213 β = 90 c = 61.888 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 ADSC CCD 2006-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.5 62.02 99.9 0.06 7.21 13.6 23994 2
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 1.5 1.58 100 0.17 14
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 1.5 42.8 22715 1226 99.8 0.184 0.182 0.1919 0.205 0.2062 RANDOM 8.85
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] 0.56 -0.3 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.93 r_dihedral_angle_4_deg 11.902 r_dihedral_angle_3_deg 9.953 r_dihedral_angle_1_deg 5.382 r_scangle_it 1.149 r_angle_refined_deg 0.985 r_scbond_it 0.816 r_angle_other_deg 0.713 r_mcangle_it 0.506 r_mcbond_it 0.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.93 r_dihedral_angle_4_deg 11.902 r_dihedral_angle_3_deg 9.953 r_dihedral_angle_1_deg 5.382 r_scangle_it 1.149 r_angle_refined_deg 0.985 r_scbond_it 0.816 r_angle_other_deg 0.713 r_mcangle_it 0.506 r_mcbond_it 0.444 r_symmetry_vdw_other 0.217 r_nbd_refined 0.187 r_nbtor_refined 0.17 r_nbd_other 0.167 r_symmetry_hbond_refined 0.098 r_symmetry_vdw_refined 0.081 r_nbtor_other 0.077 r_xyhbond_nbd_refined 0.073 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 100 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing