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Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 PROTEIN WAS CRYSTALLIZED FROM 50 MM TRIS-CL (PH 9-9.5), 10 MM NICL2, 12.5% GLYCEROL, AND 20% POLYETHYLENE GLYCOL 2000 MONOMETHYL ETHER
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.938 α = 90 b = 99.448 β = 100.57 c = 58.519 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 CCD QUANTUM-4 2X2 ARRAY MIRRORS 2002-02-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9786,0.9788 ALS 5.0.2
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 1.95 50 100 0.094 18.4 7.5 29176 2.6
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 1.95 1.98 100 0.896 2.6 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.95 50 27660 1477 99.6 0.186 0.227 RANDOM 17.1
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] 1.09 0.51 -1.6 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.389 r_scangle_it 5.155 r_scbond_it 3.506 r_mcangle_it 1.737 r_angle_refined_deg 1.673 r_mcbond_it 0.938 r_angle_other_deg 0.892 r_symmetry_vdw_other 0.306 r_symmetry_vdw_refined 0.267 r_nbd_other 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.389 r_scangle_it 5.155 r_scbond_it 3.506 r_mcangle_it 1.737 r_angle_refined_deg 1.673 r_mcbond_it 0.938 r_angle_other_deg 0.892 r_symmetry_vdw_other 0.306 r_symmetry_vdw_refined 0.267 r_nbd_other 0.247 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.194 r_symmetry_hbond_refined 0.188 r_chiral_restr 0.1 r_nbtor_other 0.087 r_metal_ion_refined 0.047 r_bond_refined_d 0.019 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3239 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 16
Software Software Software Name Purpose Quanta model building SCALEPACK data scaling CNS phasing CCP4 phasing SHARP phasing Quanta phasing REFMAC refinement