☰ Navigation Tabs
2.85 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenosine and NAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OND PDB-3OND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 19.7 mg/ml, 0.1M Tris HCl (pH 8.3), ADN, NAD;
Screen: Classics II (G4), 0.2M Lithium sulfate, 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.71 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.837 α = 90 b = 185.31 β = 97.85 c = 122.439 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD C(111) 2015-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.85 30 99.9 0.107 0.107 12.5 3.8 109105 -3 65.8
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 2.85 2.9 100 0.6 2.6 3.8
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-3OND 2.85 29.93 103575 5493 98.38 0.17439 0.173 0.1737 0.20047 0.2004 RANDOM 60.934
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] 3.59 1.03 -2.98 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.042 r_dihedral_angle_4_deg 13.453 r_dihedral_angle_3_deg 11.379 r_long_range_B_refined 5.908 r_long_range_B_other 5.88 r_scangle_other 3.764 r_mcangle_it 3.159 r_mcangle_other 3.158 r_dihedral_angle_1_deg 2.406 r_scbond_it 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.042 r_dihedral_angle_4_deg 13.453 r_dihedral_angle_3_deg 11.379 r_long_range_B_refined 5.908 r_long_range_B_other 5.88 r_scangle_other 3.764 r_mcangle_it 3.159 r_mcangle_other 3.158 r_dihedral_angle_1_deg 2.406 r_scbond_it 2.266 r_scbond_other 2.254 r_mcbond_it 1.873 r_mcbond_other 1.872 r_angle_refined_deg 1.732 r_angle_other_deg 1.462 r_chiral_restr 0.097 r_gen_planes_refined 0.014 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31050 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 548
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling BALBES phasing