2OML

crystal structure of E. coli pseudouridine synthase RluE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52944 mg/ml protein in 10 mM Tris, pH 7.5, 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate, crystals were improved by microseeding a solution of 18-22% MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate and 2 mg/ml protein at pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
1.9536.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.31α = 90
b = 56.78β = 90
c = 91.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4double crystal monochrometer2003-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.24098.10.06313.74.652181-3-310.3
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)
1.21.24940.7132.13.54929

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1KSV with N-terminal domain removed1.228.08495764957649821000.1520.1520.1490.179RANDOM11.18
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]
-0.020.09-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.185
r_dihedral_angle_4_deg16.964
r_dihedral_angle_3_deg12.083
r_sphericity_free7.981
r_dihedral_angle_1_deg6.227
r_scangle_it4.705
r_scbond_it3.851
r_sphericity_bonded3.75
r_mcangle_it2.475
r_mcbond_it2.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.185
r_dihedral_angle_4_deg16.964
r_dihedral_angle_3_deg12.083
r_sphericity_free7.981
r_dihedral_angle_1_deg6.227
r_scangle_it4.705
r_scbond_it3.851
r_sphericity_bonded3.75
r_mcangle_it2.475
r_mcbond_it2.095
r_rigid_bond_restr2.071
r_angle_refined_deg1.672
r_angle_other_deg1.459
r_mcbond_other0.666
r_symmetry_vdw_other0.332
r_nbd_refined0.222
r_nbd_other0.217
r_xyhbond_nbd_refined0.214
r_symmetry_vdw_refined0.19
r_nbtor_refined0.177
r_chiral_restr0.119
r_symmetry_hbond_refined0.094
r_nbtor_other0.087
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1443
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms30

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSphasing