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Crystal structure of a dimethyladenosine transferase from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 297 23.5% PEG3350, 0.2M Tri Lithium Citrate, 0.1M Hepes
at pH7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.008 α = 90 b = 82.222 β = 112.04 c = 75.909 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 Si(111) 2006-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.979 CHESS A1
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 1.9 50 98.9 0.078 0.078 9.8 5 55385 55385
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) 1.9 1.93 87.4 0.474 0.474 1.95 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZQ9 1.89 50 52513 52513 2825 98.07 0.20111 0.19843 0.1963 0.24954 0.2471 RANDOM 29.872
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 -2.08 1.73 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.782 r_dihedral_angle_4_deg 15.674 r_dihedral_angle_3_deg 14.787 r_dihedral_angle_1_deg 5.662 r_scangle_it 4.449 r_scbond_it 2.942 r_mcangle_it 1.813 r_angle_refined_deg 1.459 r_mcbond_it 1.156 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.782 r_dihedral_angle_4_deg 15.674 r_dihedral_angle_3_deg 14.787 r_dihedral_angle_1_deg 5.662 r_scangle_it 4.449 r_scbond_it 2.942 r_mcangle_it 1.813 r_angle_refined_deg 1.459 r_mcbond_it 1.156 r_nbtor_refined 0.307 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 4398 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling PHASER phasing