5TJ9

2.6 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Aristeromycin and NAD


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM NAD, 1mM Aristeromycin; Screen: Classics II (F9), 0.2M Ammonium sulfate, 0.1M Tris-HCL (pH 8.5), 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.331α = 90
b = 184.904β = 107.8
c = 102.508γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6301000.0950.09514.54.572106-355.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.641000.6840.7042.14.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5HM82.629.8868278374199.910.170640.16810.2183RANDOM56.924
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]
-2.340.870.161.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.815
r_dihedral_angle_3_deg9.14
r_dihedral_angle_4_deg6.956
r_long_range_B_refined4.866
r_long_range_B_other4.858
r_scangle_other2.969
r_mcangle_it2.844
r_mcangle_other2.844
r_dihedral_angle_1_deg2.213
r_scbond_it1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.815
r_dihedral_angle_3_deg9.14
r_dihedral_angle_4_deg6.956
r_long_range_B_refined4.866
r_long_range_B_other4.858
r_scangle_other2.969
r_mcangle_it2.844
r_mcangle_other2.844
r_dihedral_angle_1_deg2.213
r_scbond_it1.78
r_scbond_other1.78
r_mcbond_it1.67
r_mcbond_other1.67
r_angle_refined_deg1.452
r_angle_other_deg0.899
r_chiral_restr0.083
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.008
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms15624
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms383

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing