3DT2

The structure of rat cytosolic PEPCK in complex with oxalate and GTP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop vapor diffusion7.429812-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, hanging drop vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1943.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.423α = 90
b = 84.906β = 90
c = 119.027γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-11-29SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
11.510099.90.0939.26.998885
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)
11.51.5599.60.695.79797

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.533.1798782493699.820.160.1590.185RANDOM11.728
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]
-0.040.030.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.221
r_dihedral_angle_4_deg16.079
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg5.9
r_scangle_it3.064
r_scbond_it1.885
r_angle_refined_deg1.396
r_mcangle_it1.194
r_mcbond_it0.676
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.221
r_dihedral_angle_4_deg16.079
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg5.9
r_scangle_it3.064
r_scbond_it1.885
r_angle_refined_deg1.396
r_mcangle_it1.194
r_mcbond_it0.676
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4876
Nucleic Acid Atoms
Solvent Atoms848
Heterogen Atoms51

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling