4ODJ

Crystal structure of a putative S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with S-adenosyl-methionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SO4PDB entry 3SO4 modified with CCP4 program chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2290Microlytics MCSG1 screen, g11: 100mM Na2HPO4/citric acid pH 4.2, 40% PEG 300; CrhoA.00729.a.B1.PW37315 at 28.4mg/ml + 2.5mM S-Adenosyl-Methionine; tray 247830, puck QJI2-2, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3647.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.86α = 90
b = 117.86β = 90
c = 54.04γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252013-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.65099.50.05814.333.75707856815-324.262
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6499.50.562.39

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 entry 3SO4 modified with CCP4 program chainsaw1.6505707856815280399.530.14560.14450.1652RANDOM20.8199
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]
0.110.050.11-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.576
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg12.14
r_dihedral_angle_1_deg6.013
r_angle_refined_deg1.645
r_mcangle_it1.392
r_mcbond_it0.845
r_mcbond_other0.845
r_angle_other_deg0.824
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.576
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg12.14
r_dihedral_angle_1_deg6.013
r_angle_refined_deg1.645
r_mcangle_it1.392
r_mcbond_it0.845
r_mcbond_other0.845
r_angle_other_deg0.824
r_chiral_restr0.104
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2934
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms42

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction