5FH3

The structure of rat cytosolic PEPCK variant E89A in complex with oxalic acid and GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DT4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429825% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GTP
Crystal Properties
Matthews coefficientSolvent content
2.2745.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.699α = 90
b = 119.313β = 107.95
c = 60.821γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.97SSRLBL7-1

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
11.610098.70.06916.25.980122
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)
11.61.6691.50.3085.27417

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 REPLACEMENTTHROUGHOUT3DT41.659.6676005400998.530.20680.20480.2428RANDOM22.103
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.782
r_dihedral_angle_4_deg15.509
r_dihedral_angle_3_deg13.759
r_dihedral_angle_1_deg6.767
r_mcangle_it2.288
r_angle_refined_deg1.436
r_mcbond_it1.377
r_mcbond_other1.377
r_angle_other_deg0.883
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.782
r_dihedral_angle_4_deg15.509
r_dihedral_angle_3_deg13.759
r_dihedral_angle_1_deg6.767
r_mcangle_it2.288
r_angle_refined_deg1.436
r_mcbond_it1.377
r_mcbond_other1.377
r_angle_other_deg0.883
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4802
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms74

Software

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