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Crystal structure of a ribosomal RNA methyltransferase, putative, from Plasmodium falciparum (PF13_0052).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYU PDB entry 2NYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 298 24% PEG 3350, 0.1 M (NH4)2SO4, 0.1 M Bis-Tris pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.595 α = 90 b = 59.798 β = 90 c = 71.295 γ = 90
Symmetry Space Group P 21 21 21
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 270 2007-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91770 CHESS F1
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 1.7 50 98.5 0.073 0.065 9.9 6.8 20472 20472
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 1.7 1.76 87.9 0.324 0.284 3.7 5.4 1782
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 (All) 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 PDB entry 2NYU 1.7 45.83 20366 20366 1042 98.65 0.205 0.205 0.202 0.199 0.247 0.2464 RANDOM 20.927
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.665 r_dihedral_angle_4_deg 19.574 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 6.522 r_scangle_it 3.759 r_scbond_it 2.562 r_mcangle_it 1.684 r_angle_refined_deg 1.522 r_mcbond_it 1.043 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.665 r_dihedral_angle_4_deg 19.574 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 6.522 r_scangle_it 3.759 r_scbond_it 2.562 r_mcangle_it 1.684 r_angle_refined_deg 1.522 r_mcbond_it 1.043 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.233 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1472 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 32
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction