3PGP

Crystal structure of PA4794 - GNAT superfamily protein in complex with AcCoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I6C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52931.5 M Ammonium Sulfate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.448.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.673α = 90
b = 76.286β = 90
c = 39.311γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2009-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9792APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.425097.20.0430.32158.66.33258432584-317.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.441000.3210.3215.45.31633

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 REPLACEMENTTHROUGHOUT2i6c1.4246.013070030700163496.570.173830.173830.172290.20219RANDOM19.272
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]
-0.920.360.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.628
r_dihedral_angle_4_deg14.294
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg5.768
r_scangle_it4.177
r_scbond_it2.814
r_angle_refined_deg2.01
r_mcangle_it1.854
r_mcbond_it1.173
r_angle_other_deg1.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.628
r_dihedral_angle_4_deg14.294
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg5.768
r_scangle_it4.177
r_scbond_it2.814
r_angle_refined_deg2.01
r_mcangle_it1.854
r_mcbond_it1.173
r_angle_other_deg1.004
r_mcbond_other0.419
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1230
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms80

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-3000phasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling