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2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with D-Eritadenine 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 8.5 292 Protein: 7.9 MG/ML, 0.5M SODIUM CHLORIDE, 0.1M TRIS HCL (PH 8.3), DEA;
Screen: JCSG+ (A11), 0.2M Ammonium phosphate, 0.1M TRIS-HCL (pH 8.5), 50% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.847 α = 90 b = 121.218 β = 90 c = 178.77 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 100 CCD MARMOSAIC 300 mm CCD C(111) 2016-04-14 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) CC (Half) 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 2.15 30 100 0.1 0.1 0.887 20.2 7.5 136687 -3 32.1
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 2.15 2.19 100 0.691 3 7.4
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 5HM8 2.15 29.97 129766 6830 99.86 0.14415 0.14219 0.155 0.18125 0.188 RANDOM 40.237
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] -1.83 4.79 -2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.76 r_dihedral_angle_3_deg 10.403 r_dihedral_angle_4_deg 8.828 r_long_range_B_refined 6.712 r_long_range_B_other 6.711 r_scangle_other 3.557 r_dihedral_angle_1_deg 3.143 r_mcangle_it 2.769 r_mcangle_other 2.769 r_scbond_it 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.76 r_dihedral_angle_3_deg 10.403 r_dihedral_angle_4_deg 8.828 r_long_range_B_refined 6.712 r_long_range_B_other 6.711 r_scangle_other 3.557 r_dihedral_angle_1_deg 3.143 r_mcangle_it 2.769 r_mcangle_other 2.769 r_scbond_it 2.21 r_scbond_other 2.21 r_mcbond_it 1.669 r_mcbond_other 1.667 r_angle_refined_deg 1.498 r_angle_other_deg 0.911 r_chiral_restr 0.093 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 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 15562 Nucleic Acid Atoms Solvent Atoms 1223 Heterogen Atoms 330
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing