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Apo-form of T. thermophilus ribosomal protein L11 methyltransferase (PrmA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting-drop vapor diffusion and microseeding 6.8 298 700mM ammonium sulfate, 4%v/v Dioxane, 220mM Hexanediol, 20mM MES, pH 6.8, sitting-drop vapor diffusion and microseeding, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.521 α = 90 b = 76.557 β = 130.01 c = 61.878 γ = 90
Symmetry Space Group C 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 4 2005-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9797 NSLS X4A
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 1.59 30 96.2 0.057 17.96 3 37520 -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 1.59 1.65 91.2 0.385 2.6 2.7 3532
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 1ufk 1.59 30 35627 1889 96.09 0.1939 0.19229 0.1916 0.22405 0.2198 RANDOM 26.963
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] -0.8 -0.71 1.21 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.079 r_dihedral_angle_3_deg 16.033 r_dihedral_angle_4_deg 12.276 r_dihedral_angle_1_deg 6.006 r_scangle_it 3.967 r_scbond_it 2.523 r_angle_refined_deg 1.523 r_mcangle_it 1.507 r_mcbond_it 0.929 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.079 r_dihedral_angle_3_deg 16.033 r_dihedral_angle_4_deg 12.276 r_dihedral_angle_1_deg 6.006 r_scangle_it 3.967 r_scbond_it 2.523 r_angle_refined_deg 1.523 r_mcangle_it 1.507 r_mcbond_it 0.929 r_nbtor_refined 0.31 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.119 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1923 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling COMO phasing