3EC4

Crystal structure of Putative Acetyltransferase from the GNAT family (YP_497011.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.80 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.4327733.8% polyethylene glycol 4000, 0.2M sodium acetate, 0.1M TRIS pH 8.43, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.523α = 90
b = 63.984β = 90
c = 143.149γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-07-31MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97837SSRLBL11-1

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
11.829.2199.90.1040.1045.6283.63879917.581
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)
11.81.851000.5050.5051.53.72849

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.829.2138743194199.780.1730.1710.215RANDOM29.719
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]
0.02-1.221.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.661
r_dihedral_angle_4_deg14.231
r_dihedral_angle_3_deg12.072
r_dihedral_angle_1_deg5.845
r_scangle_it5.116
r_scbond_it3.988
r_mcangle_it2.613
r_mcbond_it1.868
r_angle_refined_deg1.563
r_angle_other_deg1.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.661
r_dihedral_angle_4_deg14.231
r_dihedral_angle_3_deg12.072
r_dihedral_angle_1_deg5.845
r_scangle_it5.116
r_scbond_it3.988
r_mcangle_it2.613
r_mcbond_it1.868
r_angle_refined_deg1.563
r_angle_other_deg1.004
r_mcbond_other0.712
r_nbd_other0.222
r_symmetry_vdw_other0.22
r_nbd_refined0.217
r_nbtor_refined0.178
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.15
r_symmetry_vdw_refined0.109
r_chiral_restr0.096
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3324
Nucleic Acid Atoms
Solvent Atoms493
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing