2Z28

Thr109Val dihydroorotase from E. coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2527717% PEG3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.378α = 90
b = 78.413β = 90
c = 179.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2005-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.874095.90.06422.74.6585535855325.5
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)
11.871.9297.80.1896.42.84336

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1XGE1.87405855358553296095.870.156060.154280.1891RANDOM27.965
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]
-0.612.55-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.504
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg11.87
r_dihedral_angle_1_deg6.191
r_scangle_it5.668
r_scbond_it4.305
r_mcangle_it4.043
r_mcbond_it3.737
r_angle_refined_deg1.398
r_mcbond_other1.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.504
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg11.87
r_dihedral_angle_1_deg6.191
r_scangle_it5.668
r_scbond_it4.305
r_mcangle_it4.043
r_mcbond_it3.737
r_angle_refined_deg1.398
r_mcbond_other1.198
r_angle_other_deg0.84
r_symmetry_vdw_other0.219
r_nbd_refined0.215
r_symmetry_hbond_refined0.209
r_nbd_other0.184
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.119
r_symmetry_vdw_refined0.101
r_chiral_restr0.084
r_nbtor_other0.083
r_metal_ion_refined0.022
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5331
Nucleic Acid Atoms
Solvent Atoms506
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling