2RKD

The Structure of rat cytosolic PEPCK in complex with 3-phosphonopropionate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429812-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2444.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.294α = 90
b = 119.397β = 108.66
c = 60.762γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray118IMAGE PLATERIGAKU RAXIS IV++BLUE OSMIC Confocal MIRRORS2007-06-23SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.910097.20.09214.9746838
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)
11.91.9784.20.6535.54065

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 DIFFRACTIONTHROUGHOUT1.933.9846794237797.110.1890.1870.233RANDOM15.395
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]
0.030.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.195
r_dihedral_angle_4_deg15.192
r_dihedral_angle_3_deg15.043
r_dihedral_angle_1_deg5.749
r_scangle_it1.711
r_angle_refined_deg1.112
r_scbond_it1.038
r_mcangle_it0.669
r_mcbond_it0.362
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.195
r_dihedral_angle_4_deg15.192
r_dihedral_angle_3_deg15.043
r_dihedral_angle_1_deg5.749
r_scangle_it1.711
r_angle_refined_deg1.112
r_scbond_it1.038
r_mcangle_it0.669
r_mcbond_it0.362
r_nbtor_refined0.301
r_nbd_refined0.18
r_symmetry_vdw_refined0.16
r_metal_ion_refined0.136
r_symmetry_hbond_refined0.121
r_xyhbond_nbd_refined0.12
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4819
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection