6LTV

Crystal Structure of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with ONB-SAM (2-nitro benzyme S-adenosyl-methionine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ODJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5285.1512.5 % MPD (v/v), 12.5 % PEG 1000 (w/v) , 12.5 % PEG 3350 (w/v), 0.1 MES/imidazole pH 6.5, 0.03 M sodium phosphate dibasic dihydrate, 0.03 M ammonium sulfate and 0.03 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.346.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.169α = 90
b = 100.167β = 95.99
c = 66.945γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8748.2899.10.0950.1040.0410.99715.26.667224
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.9291.70.7760.8440.3270.8376.3

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 REPLACEMENTTHROUGHOUT4ODJ1.8748.2863811338499.130.16390.16230.1941RANDOM29.952
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]
1.720.17-1.69-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.306
r_dihedral_angle_4_deg16.477
r_dihedral_angle_3_deg14.981
r_dihedral_angle_1_deg7.1
r_angle_refined_deg2.378
r_angle_other_deg1.057
r_chiral_restr0.149
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.306
r_dihedral_angle_4_deg16.477
r_dihedral_angle_3_deg14.981
r_dihedral_angle_1_deg7.1
r_angle_refined_deg2.378
r_angle_other_deg1.057
r_chiral_restr0.149
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5893
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction