5TLS

2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with DZ2002 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 ZD2002, 1mM NAD; Screen: JCSG+ (A11), 0.2M Ammonium phosphate, 0.1M Tris-HCL (pH 8.5), 50% (v/v) MPD.
Crystal Properties
Matthews coefficientSolvent content
3.0960.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.52α = 90
b = 133.027β = 90
c = 174.86γ = 90
Symmetry
Space GroupP 21 21 21

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
12.4301000.1020.10216.85.9109137-343.3
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)
12.42.4499.90.7340.8922.65.7

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 REPLACEMENTTHROUGHOUT5HM82.429.95102888544599.880.151780.149930.1871RANDOM49.872
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]
3.142.85-5.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.355
r_dihedral_angle_3_deg9.587
r_dihedral_angle_4_deg8.892
r_long_range_B_refined5.523
r_long_range_B_other5.433
r_scangle_other2.759
r_mcangle_it2.623
r_mcangle_other2.623
r_dihedral_angle_1_deg2.569
r_scbond_it1.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.355
r_dihedral_angle_3_deg9.587
r_dihedral_angle_4_deg8.892
r_long_range_B_refined5.523
r_long_range_B_other5.433
r_scangle_other2.759
r_mcangle_it2.623
r_mcangle_other2.623
r_dihedral_angle_1_deg2.569
r_scbond_it1.705
r_scbond_other1.646
r_mcbond_it1.534
r_mcbond_other1.534
r_angle_refined_deg1.505
r_angle_other_deg0.913
r_chiral_restr0.092
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.009
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms15619
Nucleic Acid Atoms
Solvent Atoms1036
Heterogen Atoms342

Software

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