5FH4

The structure of rat cytosolic PEPCK variant E89D in complex with beta-sulfopyruvate and GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DT7 

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
2.1843.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.59α = 90
b = 118.809β = 109.3
c = 60.508γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.9SSRLBL7-1

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
11.4910099.90.088136.195906
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)
11.51.5599.90.5125.99625

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 REPLACEMENTTHROUGHOUT3DT71.4934.3490947478799.10.20560.20440.2286RANDOM23.33
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]
-0.39-0.16-0.010.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.177
r_dihedral_angle_4_deg16.611
r_dihedral_angle_3_deg12.763
r_dihedral_angle_1_deg6.398
r_angle_refined_deg1.621
r_angle_other_deg0.968
r_mcangle_it0.374
r_mcbond_it0.209
r_mcbond_other0.209
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.177
r_dihedral_angle_4_deg16.611
r_dihedral_angle_3_deg12.763
r_dihedral_angle_1_deg6.398
r_angle_refined_deg1.621
r_angle_other_deg0.968
r_mcangle_it0.374
r_mcbond_it0.209
r_mcbond_other0.209
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4811
Nucleic Acid Atoms
Solvent Atoms502
Heterogen Atoms54

Software

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