4YWD

Structure of rat cytosolic pepck in complex with 2,3-Pyridine dicarboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QEWPDB ENTRY 2QEW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429825% PEG 3350, 0.1M HEPES PH 7.4,2 MM MNCL2, 1MM 2,3-PYRIDINE DICARBOXYLIC ACID, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.2445.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.34α = 90
b = 119.405β = 109.16
c = 61.015γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MIRRORS2011-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
12.110092.90.09710.74.633335
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)
12.12.1863.80.5193.8

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 2QEW2.157.6333269167892.80.1970.1950.237RANDOM50.87
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]
-1.080.6-0.671.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.551
r_dihedral_angle_3_deg13.802
r_dihedral_angle_4_deg13.445
r_dihedral_angle_1_deg6.006
r_angle_refined_deg1.081
r_angle_other_deg0.705
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.551
r_dihedral_angle_3_deg13.802
r_dihedral_angle_4_deg13.445
r_dihedral_angle_1_deg6.006
r_angle_refined_deg1.081
r_angle_other_deg0.705
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.004
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4754
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms15

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling