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2.65 Angstrom Resolution Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with SAH and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 9.3 mg/ml, 0.5M Sodium chloride, 0.1M Tris HCl (pH 8.3), 1mM Adenosine, 1mM NAD, 1mM Homocysteine;
Screen: Classics II (F6), 0.2M Ammonium sulfate, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.69 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.906 α = 90 b = 185.834 β = 97.98 c = 121.619 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 225 mm CCD C(111) 2016-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 2.65 30 100 0.099 0.099 0.047 16.2 5.2 137384 -3 58.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 100 0.646 0.646 0.307 0.843 2.8 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HM8 2.65 30 130306 6930 99.91 0.172 0.17041 0.20208 0.1947 RANDOM 52.2
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] 0.74 -0.55 -2.47 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.326 r_dihedral_angle_4_deg 13.195 r_dihedral_angle_3_deg 11.373 r_long_range_B_refined 5.86 r_long_range_B_other 5.847 r_scangle_other 3.796 r_mcangle_it 3.187 r_mcangle_other 3.187 r_dihedral_angle_1_deg 2.643 r_scbond_it 2.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.326 r_dihedral_angle_4_deg 13.195 r_dihedral_angle_3_deg 11.373 r_long_range_B_refined 5.86 r_long_range_B_other 5.847 r_scangle_other 3.796 r_mcangle_it 3.187 r_mcangle_other 3.187 r_dihedral_angle_1_deg 2.643 r_scbond_it 2.392 r_scbond_other 2.39 r_mcbond_it 1.922 r_mcbond_other 1.921 r_angle_refined_deg 1.586 r_angle_other_deg 0.91 r_chiral_restr 0.089 r_gen_planes_refined 0.023 r_gen_planes_other 0.02 r_bond_refined_d 0.009 r_bond_other_d 0.001 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 31128 Nucleic Acid Atoms Solvent Atoms 931 Heterogen Atoms 837
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing