2PYU

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K7KPDB CODE 1K7K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29820% PEG3350, 200 mM Mg Acetate, cryoprotected with 7% each of glycerol, sucrose and ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.941α = 90
b = 77.941β = 90
c = 81.073γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic Mirrors2006-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.025099.90.05737.54.9319243148830.6
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)
12.022.0999.60.4765.54.73168

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB CODE 1K7K2.0232.031611986099.940.195060.195060.192240.25346RANDOM32.283
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]
0.020.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.935
r_dihedral_angle_4_deg21.644
r_dihedral_angle_3_deg14.233
r_dihedral_angle_1_deg7.032
r_scangle_it5.629
r_scbond_it3.814
r_mcangle_it2.298
r_angle_refined_deg2.236
r_mcbond_it1.517
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.935
r_dihedral_angle_4_deg21.644
r_dihedral_angle_3_deg14.233
r_dihedral_angle_1_deg7.032
r_scangle_it5.629
r_scbond_it3.814
r_mcangle_it2.298
r_angle_refined_deg2.236
r_mcbond_it1.517
r_nbtor_refined0.312
r_nbd_refined0.229
r_symmetry_vdw_refined0.229
r_chiral_restr0.163
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.112
r_bond_refined_d0.026
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1559
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing