4M6V

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


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% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 345 mM Tetramethylammonium chloride, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9257.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.641α = 90
b = 157.828β = 90
c = 244.953γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12706APS21-ID-D

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
12.45099.80.06925.77.2128300128103-3
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)
12.42.4699.80.4055.27.1

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 4JX42.449.66121746644899.620.185680.183690.22319RANDOM62.797
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]
5.58-1.04-4.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.222
r_dihedral_angle_4_deg18.638
r_dihedral_angle_3_deg14.923
r_dihedral_angle_1_deg5.802
r_long_range_B_refined4.13
r_long_range_B_other4.127
r_scangle_other2.592
r_mcangle_it2.563
r_mcangle_other2.563
r_scbond_it1.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.222
r_dihedral_angle_4_deg18.638
r_dihedral_angle_3_deg14.923
r_dihedral_angle_1_deg5.802
r_long_range_B_refined4.13
r_long_range_B_other4.127
r_scangle_other2.592
r_mcangle_it2.563
r_mcangle_other2.563
r_scbond_it1.676
r_scbond_other1.676
r_mcbond_it1.615
r_mcbond_other1.615
r_angle_refined_deg1.385
r_angle_other_deg0.801
r_chiral_restr0.074
r_bond_refined_d0.011
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17838
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms206

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling