☰ Navigation Tabs
T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in complex with ribosomal protein L11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MMS pdb entries 1MMS, 2NXC experimental model PDB 2NXC pdb entries 1MMS, 2NXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 25.5 % w/v PEG4000, 120 mM Sodium Acetate, 85mM TRIS, pH 8.5, 15 % v/v glycerol, 4% v/v 1,1,1,3,3,3-Hexafluoro-2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.844 α = 90 b = 132.844 β = 90 c = 46.006 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 MAR scanner 345 mm plate 2006-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C NSLS X4C
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 2.4 30 98.9 0.077 17.6 4.3 18545 18330 -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 2.4 2.49 96.9 0.395 2.8 3.3 1766
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 1MMS, 2NXC 2.4 30 17325 940 99 0.22273 0.2202 0.2149 0.27277 0.2688 RANDOM 62.672
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] -0.18 -0.09 -0.18 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.43 r_dihedral_angle_3_deg 21.56 r_dihedral_angle_4_deg 18.186 r_dihedral_angle_1_deg 7.038 r_scangle_it 2.755 r_angle_refined_deg 1.747 r_scbond_it 1.742 r_mcangle_it 1.172 r_mcbond_it 0.733 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.43 r_dihedral_angle_3_deg 21.56 r_dihedral_angle_4_deg 18.186 r_dihedral_angle_1_deg 7.038 r_scangle_it 2.755 r_angle_refined_deg 1.747 r_scbond_it 1.742 r_mcangle_it 1.172 r_mcbond_it 0.733 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.118 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2959 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling COMO phasing PHASER phasing