2BX7

Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,5-dihydroxybenzoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OVDPDB ENTRY 1OVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.8HANGING DROPS OF 2 MICROLITERS PROTEIN AND INHIBITOR (17 MG/ML PROTEIN AND 2.6 MM 3, 5-DIHYDROXYBENZOATE) AND 2 MIKROLITERS RESERVOIR. DROPS WERE EQUILIBRATED OVER 1 ML RESERVOIR SOLUTION. RESERVOIR SOLUTION: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL, PH 8.8
Crystal Properties
Matthews coefficientSolvent content
2.5751.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.71α = 90
b = 108.127β = 104.06
c = 66.216γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
12.032593.10.0821.53.947526
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)
12.032.0847.50.346.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1OVD2.042541966223694.80.1870.1840.229RANDOM28.46
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]
3.76-0.52-2.42-1.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.571
r_scangle_it3.839
r_scbond_it2.377
r_mcangle_it1.561
r_angle_refined_deg1.528
r_angle_other_deg0.882
r_mcbond_it0.843
r_nbd_other0.237
r_nbd_refined0.217
r_symmetry_vdw_refined0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.571
r_scangle_it3.839
r_scbond_it2.377
r_mcangle_it1.561
r_angle_refined_deg1.528
r_angle_other_deg0.882
r_mcbond_it0.843
r_nbd_other0.237
r_nbd_refined0.217
r_symmetry_vdw_refined0.2
r_symmetry_vdw_other0.164
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.137
r_chiral_restr0.095
r_nbtor_other0.084
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4818
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling