4LOC

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxamate and biotin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JX4PDB ENTRY 4JX4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH CRYSTALLIZATION UNDER OIL629814% (w/v) PEG 8000, 110 mM MOPS (pH 6.0), 165 mM Tetramethylammonium chloride, 2% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8857.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.87α = 90
b = 157.123β = 90
c = 244.714γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.265098.30.08420.67.1148360145868-334.4
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)
12.262.394.70.4443.46.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4JX42.2643.75140726744497.970.178370.176350.21628RANDOM50.934
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]
4.52-1.78-2.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.428
r_dihedral_angle_4_deg19.813
r_dihedral_angle_3_deg15.782
r_dihedral_angle_1_deg6.359
r_long_range_B_refined5.794
r_long_range_B_other5.794
r_scangle_other2.931
r_mcangle_it2.462
r_mcangle_other2.462
r_scbond_it2.241
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.428
r_dihedral_angle_4_deg19.813
r_dihedral_angle_3_deg15.782
r_dihedral_angle_1_deg6.359
r_long_range_B_refined5.794
r_long_range_B_other5.794
r_scangle_other2.931
r_mcangle_it2.462
r_mcangle_other2.462
r_scbond_it2.241
r_scbond_other2.241
r_angle_refined_deg1.836
r_mcbond_it1.656
r_mcbond_other1.655
r_angle_other_deg0.896
r_chiral_restr0.1
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17888
Nucleic Acid Atoms
Solvent Atoms535
Heterogen Atoms111

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling