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2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Neplanocin-A and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HM8 PDB-5HM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3),1mM NeplanocinA;
Screen: Classics II (D7), 0.1M Bis-Tris-HCL (pH 6.5), 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.885 α = 90 b = 136.486 β = 95.73 c = 107.805 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) 2016-04-18 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) 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 2.25 30 99.8 0.078 0.078 0.87 17.1 4.4 96622 -3 41.6
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 2.25 2.29 99.8 0.662 2.5 4.2
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-5HM8 2.25 29.93 91403 4857 99.64 0.1758 0.17341 0.1769 0.22103 0.222 RANDOM 48.575
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] 3.12 4.32 -2.58 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.13 r_dihedral_angle_4_deg 10.169 r_dihedral_angle_3_deg 9.998 r_long_range_B_refined 6.389 r_long_range_B_other 6.36 r_scangle_other 2.91 r_dihedral_angle_1_deg 2.852 r_mcangle_it 2.667 r_mcangle_other 2.666 r_scbond_it 1.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.13 r_dihedral_angle_4_deg 10.169 r_dihedral_angle_3_deg 9.998 r_long_range_B_refined 6.389 r_long_range_B_other 6.36 r_scangle_other 2.91 r_dihedral_angle_1_deg 2.852 r_mcangle_it 2.667 r_mcangle_other 2.666 r_scbond_it 1.794 r_scbond_other 1.794 r_mcbond_it 1.6 r_mcbond_other 1.599 r_angle_refined_deg 1.469 r_angle_other_deg 0.893 r_chiral_restr 0.086 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.008 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 15383 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms 338
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing