5T8K

1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine and NAD


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5292Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM Adenine, 1mM NAD, 1mM Homocysteine, Screen: Classics II (D9), 0.1M Bis-Tris-HCL (pH 8.5), 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.652.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.686α = 90
b = 182.785β = 100.58
c = 96.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-06-16MSINGLE 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
11.95301000.0760.07620.83.8166729-326
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)
11.951.981000.7220.6523.7

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 REPLACEMENTTHROUGHOUTPDB-5HM81.9529.92158251828399.930.14250.140920.17296RANDOM33.031
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]
-0.58-0.470.140.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.292
r_dihedral_angle_3_deg10.082
r_dihedral_angle_4_deg8.183
r_long_range_B_refined5.741
r_long_range_B_other5.473
r_dihedral_angle_1_deg3.175
r_scangle_other2.641
r_mcangle_it2.158
r_mcangle_other2.157
r_scbond_it1.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.292
r_dihedral_angle_3_deg10.082
r_dihedral_angle_4_deg8.183
r_long_range_B_refined5.741
r_long_range_B_other5.473
r_dihedral_angle_1_deg3.175
r_scangle_other2.641
r_mcangle_it2.158
r_mcangle_other2.157
r_scbond_it1.588
r_scbond_other1.588
r_angle_refined_deg1.443
r_mcbond_it1.273
r_mcbond_other1.273
r_angle_other_deg0.896
r_chiral_restr0.091
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 Atoms15562
Nucleic Acid Atoms
Solvent Atoms1925
Heterogen Atoms364

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing