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Crystal structure of a putative protein-L-isoaspartate O-methyltransferase beta-aspartate methyltransferase (PCMT) from Plasmodium falciparum in complex with S-adenosyl-L-homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L1N PDB entry 1L1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 25% 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 coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.156 α = 90 b = 75.156 β = 90 c = 77.389 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2007-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 99.1 0.1 0.074 22 5.3 33234 33234
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) Redundancy Number Unique Reflections (All) 1 2 2.07 90.7 0.899 0.713 2 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1L1N 2 33.81 31337 31337 1673 99.2 0.22644 0.22407 0.26789 0.2349 RANDOM 36.531
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] 1.46 0.73 1.46 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.433 r_dihedral_angle_4_deg 23.12 r_dihedral_angle_3_deg 16.646 r_dihedral_angle_1_deg 6.484 r_scangle_it 2.87 r_scbond_it 1.906 r_angle_refined_deg 1.503 r_mcangle_it 1.309 r_mcbond_it 0.761 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.433 r_dihedral_angle_4_deg 23.12 r_dihedral_angle_3_deg 16.646 r_dihedral_angle_1_deg 6.484 r_scangle_it 2.87 r_scbond_it 1.906 r_angle_refined_deg 1.503 r_mcangle_it 1.309 r_mcbond_it 0.761 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 3476 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing