4MIM

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with 3-bromopyruvate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH CRYSTALLIZATION UNDER OIL629811.3% (w/v) PEG 8000, 99 mM BisTris, 346 mM tetramethylammonium chloride, pH 6.0, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9257.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.592α = 90
b = 157.06β = 90
c = 243.098γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDC(111)2012-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.979APS21-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
12.655099.90.08224.57.19517595052-353.8
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)
12.652.799.70.4433.66.6

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 4JX42.6548.1390123475699.270.188670.186240.23495RANDOM72.823
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]
9.03-3.9-5.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.075
r_dihedral_angle_4_deg19.605
r_dihedral_angle_3_deg15.726
r_dihedral_angle_1_deg6.282
r_long_range_B_refined5.817
r_long_range_B_other5.815
r_scangle_other3.683
r_mcangle_it3.611
r_mcangle_other3.611
r_scbond_it2.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.075
r_dihedral_angle_4_deg19.605
r_dihedral_angle_3_deg15.726
r_dihedral_angle_1_deg6.282
r_long_range_B_refined5.817
r_long_range_B_other5.815
r_scangle_other3.683
r_mcangle_it3.611
r_mcangle_other3.611
r_scbond_it2.518
r_scbond_other2.518
r_mcbond_other2.411
r_mcbond_it2.41
r_angle_refined_deg1.612
r_angle_other_deg0.858
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms17508
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms49

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling