4BJH | pdb_00004bjh

Crystal Structure of the Aquifex Reactor Complex Formed by Dihydroorotase (H180A, H232A) with Dihydroorotate and Aspartate Transcarbamoylase with N-(phosphonacetyl)-L-aspartate (PALA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D6NPDB ENTRY 3D6N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5THE CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN HANGING-DROPS. THE HETERO DODECAMER WAS BUFFER EXCHANGED INTO 10 MM HEPES, 1 MM TCEP PH 7.5, AT A FINAL PROTEIN CONCENTRATION OF 3.0 MG/ML. DHO-ATC SOLUTION (3-6 UL) WAS MIXED WITH 1 UL OF RESERVOIR SOLUTION (30% ETHYLENE GLYCOL) FOLLOWED BY 10% OF THE DROP VOLUME (V/V) OF 100 MM BARIUM CHLORIDE. THE FINAL CRYSTALLIZATION PH WAS 6.3.
Crystal Properties
Matthews coefficientSolvent content
3.1761.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.152α = 90
b = 157.152β = 90
c = 233.244γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MAR300BE LENSES2009-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-GAPS21-ID-G

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
12.277.8599.90.116.28.85336541.7
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)
12.22.321000.762.38.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3D6N2.277.8553365284699.940.162820.160660.15720.203040.1974RANDOM41.256
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]
-0.27-0.14-0.270.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.837
r_dihedral_angle_4_deg23.094
r_dihedral_angle_3_deg15.736
r_dihedral_angle_1_deg6.491
r_scangle_it4.184
r_scbond_it2.588
r_angle_refined_deg1.558
r_mcangle_it1.423
r_mcbond_it0.738
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.837
r_dihedral_angle_4_deg23.094
r_dihedral_angle_3_deg15.736
r_dihedral_angle_1_deg6.491
r_scangle_it4.184
r_scbond_it2.588
r_angle_refined_deg1.558
r_mcangle_it1.423
r_mcbond_it0.738
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms5622
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
ARP/wARPphasing