2H1R

Crystal structure of a dimethyladenosine transferase from Plasmodium falciparum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZQ9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.129723.5% PEG3350, 0.2M Tri Lithium Citrate, 0.1M Hepes at pH7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.7855.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.008α = 90
b = 82.222β = 112.04
c = 75.909γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Si(111)2006-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.979CHESSA1

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
11.95098.90.0780.0789.855538555385
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9387.40.4740.4741.952.9

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 REPLACEMENTTHROUGHOUT1ZQ91.89505251352513282598.070.201110.198430.24954RANDOM29.872
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]
-1.44-2.081.73-1.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.782
r_dihedral_angle_4_deg15.674
r_dihedral_angle_3_deg14.787
r_dihedral_angle_1_deg5.662
r_scangle_it4.449
r_scbond_it2.942
r_mcangle_it1.813
r_angle_refined_deg1.459
r_mcbond_it1.156
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.782
r_dihedral_angle_4_deg15.674
r_dihedral_angle_3_deg14.787
r_dihedral_angle_1_deg5.662
r_scangle_it4.449
r_scbond_it2.942
r_mcangle_it1.813
r_angle_refined_deg1.459
r_mcbond_it1.156
r_nbtor_refined0.307
r_nbd_refined0.214
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.192
r_xyhbond_nbd_refined0.148
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4398
Nucleic Acid Atoms
Solvent Atoms498
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling
PHASERphasing