3ONP

Crystal Structure of tRNA/rRNA Methyltransferase SpoU from Rhodobacter sphaeroides


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62970.17 M Ammonium Acetate, 0.085 M Na Citrate pH 5.6, 25.5% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
1.9938.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.782α = 90
b = 74.782β = 90
c = 139.105γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2010-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97924APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.95099.90.0812.717.2187911879136.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9399.60.7862.5810.2904

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.950177641776496199.340.1910.1910.1890.219RANDOM40.863
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]
-0.43-0.22-0.430.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.402
r_dihedral_angle_4_deg20.397
r_dihedral_angle_3_deg18.109
r_dihedral_angle_1_deg5.663
r_scangle_it5.252
r_scbond_it3.06
r_mcangle_it2.219
r_angle_refined_deg1.505
r_mcbond_it1.209
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.402
r_dihedral_angle_4_deg20.397
r_dihedral_angle_3_deg18.109
r_dihedral_angle_1_deg5.663
r_scangle_it5.252
r_scbond_it3.06
r_mcangle_it2.219
r_angle_refined_deg1.505
r_mcbond_it1.209
r_chiral_restr0.122
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 AtomsNumber
Protein Atoms1218
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms23

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing