2Z2A

Thr109Gly dihydroorotase from E. coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2527717% PEG 3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.435α = 90
b = 78.193β = 90
c = 179.961γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2005-04-30MSINGLE 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
11.874091.90.04834.14.6560365603625.2
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)
11.871.9291.70.1528.73.94069

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 REPLACEMENTTHROUGHOUT1XGE1.87405603656036283591.940.154540.152360.19612RANDOM29.116
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]
-1.171.93-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.353
r_dihedral_angle_4_deg16.52
r_dihedral_angle_3_deg12.722
r_scangle_it7.609
r_dihedral_angle_1_deg6.267
r_scbond_it6.085
r_mcangle_it4.356
r_mcbond_it3.744
r_angle_refined_deg1.443
r_mcbond_other1.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.353
r_dihedral_angle_4_deg16.52
r_dihedral_angle_3_deg12.722
r_scangle_it7.609
r_dihedral_angle_1_deg6.267
r_scbond_it6.085
r_mcangle_it4.356
r_mcbond_it3.744
r_angle_refined_deg1.443
r_mcbond_other1.225
r_angle_other_deg0.84
r_symmetry_vdw_other0.228
r_nbd_refined0.214
r_nbd_other0.182
r_nbtor_refined0.178
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.142
r_chiral_restr0.087
r_nbtor_other0.084
r_metal_ion_refined0.024
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 Atoms5308
Nucleic Acid Atoms
Solvent Atoms583
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling