3MJM

His257Ala mutant of dihydroorotase from E. coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627715-20 % PEG 3350, 0.1 M MES pH 6.0, 150 mM KCl, 75 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3647.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.115α = 90
b = 79.063β = 90
c = 180.436γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOSMIC MIRRORS2009-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
11.865094.40.07917.23.36193859132
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)
1.861.9383.60.2762.6

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 REPLACEMENTTHROUGHOUTPDB entry 1XGE1.8745.136191956039301095.360.170890.169290.2001RANDOM23.311
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]
-1.693.78-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.017
r_dihedral_angle_4_deg15.684
r_dihedral_angle_3_deg12.027
r_dihedral_angle_1_deg6.265
r_scangle_it2.121
r_mcangle_it1.878
r_angle_refined_deg1.543
r_scbond_it1.482
r_mcbond_it1.335
r_angle_other_deg1.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.017
r_dihedral_angle_4_deg15.684
r_dihedral_angle_3_deg12.027
r_dihedral_angle_1_deg6.265
r_scangle_it2.121
r_mcangle_it1.878
r_angle_refined_deg1.543
r_scbond_it1.482
r_mcbond_it1.335
r_angle_other_deg1.003
r_mcbond_other0.415
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5274
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms35

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling