3H83

2.06 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor'


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YFZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295The Classic II Suite, condition B6, mixed with 1:1 v/v with protein sample (7.4 mg/mL, 0.25 M NaCl, 5 mM BME, 10 mM Tris/HCl pH 8.3), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8156.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.236α = 90
b = 80.549β = 101.23
c = 120.536γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe Lenses/Diamond Laue Mono2009-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.0650970.0911.853.46100761007-3
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)
12.062.199.90.2554.43

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1YFZ2.06305787057870310596.740.17040.168410.20753RANDOM19.931
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]
-1.56-0.091.450.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.545
r_dihedral_angle_3_deg12.257
r_dihedral_angle_4_deg10.979
r_scangle_it6.34
r_dihedral_angle_1_deg4.959
r_scbond_it4.097
r_mcangle_it2.65
r_angle_refined_deg1.767
r_mcbond_it1.477
r_angle_other_deg0.987
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.545
r_dihedral_angle_3_deg12.257
r_dihedral_angle_4_deg10.979
r_scangle_it6.34
r_dihedral_angle_1_deg4.959
r_scbond_it4.097
r_mcangle_it2.65
r_angle_refined_deg1.767
r_mcbond_it1.477
r_angle_other_deg0.987
r_mcbond_other0.467
r_chiral_restr0.185
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5895
Nucleic Acid Atoms
Solvent Atoms510
Heterogen Atoms119

Software

Software
Software NamePurpose
Blu-Icedata collection
BALBESphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling