1Q1K

Structure of ATP-phosphoribosyltransferase from E. coli complexed with PR-ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H3DPDB ENTRY 1H3D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6298sodium tartrate, magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8556.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.1α = 90
b = 132.1β = 90
c = 113.379γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.86SRSPX9.6

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
12.95099.30.05816.94.28521852122
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)
12.93.0299.90.58124.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 ENTRY 1H3D2.9508521783468799.240.214540.214540.209670.27243RANDOM44.098
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]
3.041.523.04-4.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.807
r_scangle_it3.842
r_scbond_it2.255
r_angle_refined_deg2.018
r_mcangle_it1.424
r_mcbond_it0.736
r_nbd_refined0.264
r_symmetry_hbond_refined0.257
r_symmetry_vdw_refined0.242
r_xyhbond_nbd_refined0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.807
r_scangle_it3.842
r_scbond_it2.255
r_angle_refined_deg2.018
r_mcangle_it1.424
r_mcbond_it0.736
r_nbd_refined0.264
r_symmetry_hbond_refined0.257
r_symmetry_vdw_refined0.242
r_xyhbond_nbd_refined0.147
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2187
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing