2PBF

Crystal structure of a putative protein-L-isoaspartate O-methyltransferase beta-aspartate methyltransferase (PCMT) from Plasmodium falciparum in complex with S-adenosyl-L-homocysteine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L1NPDB entry 1L1N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.229825% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Hepes pH 7.2, 2 mM SAH, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.156α = 90
b = 75.156β = 90
c = 77.389γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
125099.10.10.074225.33323433234
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)
122.0790.70.8990.71324.9

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 REPLACEMENTTHROUGHOUTPDB entry 1L1N233.813133731337167399.20.226440.224070.26789RANDOM36.531
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]
1.460.731.46-2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.433
r_dihedral_angle_4_deg23.12
r_dihedral_angle_3_deg16.646
r_dihedral_angle_1_deg6.484
r_scangle_it2.87
r_scbond_it1.906
r_angle_refined_deg1.503
r_mcangle_it1.309
r_mcbond_it0.761
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.433
r_dihedral_angle_4_deg23.12
r_dihedral_angle_3_deg16.646
r_dihedral_angle_1_deg6.484
r_scangle_it2.87
r_scbond_it1.906
r_angle_refined_deg1.503
r_mcangle_it1.309
r_mcbond_it0.761
r_nbtor_refined0.305
r_symmetry_vdw_refined0.243
r_nbd_refined0.204
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.126
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.005
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 Atoms3476
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms52

Software

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