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Ribosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal protein L11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NXC pdb entries 2NXC, 2NXN experimental model PDB 2NXN pdb entries 2NXC, 2NXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 5.8 277 200mM magnesium nitrate hexahydrate, 20% w/v PEG3350, 4mM AdoMet, pH 5.8, microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.822 α = 90 b = 69.943 β = 90.47 c = 379.007 γ = 90
Symmetry Space Group P 1 2 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 315 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2007-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9797 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 30 96.5 0.071 25 6.7 157914 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 76.7 0.364 2.7 4.6 12404
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 pdb entries 2NXC, 2NXN 2.3 29.74 149975 7909 96.31 0.19765 0.19442 0.1904 0.2593 0.2515 RANDOM 44.08
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.514 r_dihedral_angle_4_deg 20.195 r_dihedral_angle_3_deg 17.687 r_dihedral_angle_1_deg 6.326 r_scangle_it 2.802 r_scbond_it 1.715 r_angle_refined_deg 1.538 r_mcangle_it 1.071 r_mcbond_it 0.647 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.514 r_dihedral_angle_4_deg 20.195 r_dihedral_angle_3_deg 17.687 r_dihedral_angle_1_deg 6.326 r_scangle_it 2.802 r_scbond_it 1.715 r_angle_refined_deg 1.538 r_mcangle_it 1.071 r_mcbond_it 0.647 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.247 r_xyhbond_nbd_refined 0.243 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.211 r_chiral_restr 0.095 r_bond_refined_d 0.014 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 21338 Nucleic Acid Atoms Solvent Atoms 1885 Heterogen Atoms 296
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing