1UWV

Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19PROTEIN 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 coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.938α = 90
b = 99.448β = 100.57
c = 58.519γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD QUANTUM-4 2X2 ARRAYMIRRORS2002-02-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.9786,0.9788ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95501000.09418.47.5291762.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.981000.8962.67.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.955027660147799.60.1860.227RANDOM17.1
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]
1.090.51-1.60.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.389
r_scangle_it5.155
r_scbond_it3.506
r_mcangle_it1.737
r_angle_refined_deg1.673
r_mcbond_it0.938
r_angle_other_deg0.892
r_symmetry_vdw_other0.306
r_symmetry_vdw_refined0.267
r_nbd_other0.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.389
r_scangle_it5.155
r_scbond_it3.506
r_mcangle_it1.737
r_angle_refined_deg1.673
r_mcbond_it0.938
r_angle_other_deg0.892
r_symmetry_vdw_other0.306
r_symmetry_vdw_refined0.267
r_nbd_other0.247
r_nbd_refined0.213
r_xyhbond_nbd_refined0.194
r_symmetry_hbond_refined0.188
r_chiral_restr0.1
r_nbtor_other0.087
r_metal_ion_refined0.047
r_bond_refined_d0.019
r_gen_planes_other0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms3239
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms16

Software

Software
Software NamePurpose
Quantamodel building
SCALEPACKdata scaling
CNSphasing
CCP4phasing
SHARPphasing
Quantaphasing
REFMACrefinement