3FCK

Complex of UNG2 and a fragment-based design inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82951 MICROLITER OF THE SOLUTION: 0.001 M UNG2 0.05 M TRIS-OAC pH 7.0, 0.15 M NACL 0.001 M DTT 0.005 M INHIBITOR, WAS MIXED WITH EQUAL AMOUNT OF THE SOLUTION CONTAINING 0.16 M KSCN AND 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthew coefficientSolvent content
2.0539.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.18α = 90
b = 69.149β = 90
c = 70.037γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV2007-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.635084.90.0424.322828
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)
1.631.6914.70.5421.4384

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6427.222779112485.650.1970.1950.229RANDOM25.738
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]
0.57-0.29-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.348
r_dihedral_angle_3_deg11.989
r_dihedral_angle_4_deg11.962
r_dihedral_angle_1_deg5.239
r_scangle_it2.105
r_scbond_it1.291
r_angle_refined_deg1.01
r_mcangle_it0.837
r_mcbond_it0.478
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.348
r_dihedral_angle_3_deg11.989
r_dihedral_angle_4_deg11.962
r_dihedral_angle_1_deg5.239
r_scangle_it2.105
r_scbond_it1.291
r_angle_refined_deg1.01
r_mcangle_it0.837
r_mcbond_it0.478
r_nbtor_refined0.308
r_symmetry_vdw_refined0.198
r_nbd_refined0.193
r_symmetry_hbond_refined0.108
r_xyhbond_nbd_refined0.104
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1800
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms25

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction