3TPY

Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D4LPDB entry 2D4L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.559α = 90
b = 60.559β = 90
c = 63.635γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2003-02-09MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 315r2003-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8028EMBL/DESY, HAMBURGX13
2SYNCHROTRONESRF BEAMLINE ID14-41.0720ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1,21.752099.80.03244.811.41339913399-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.751.771000.4024.411.3438

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 DIFFRACTIONSIRASTHROUGHOUTPDB entry 2D4L1.7520133051260070599.030.15360.15170.1864RANDOM27.004
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]
0.790.40.79-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.517
r_dihedral_angle_4_deg28.651
r_dihedral_angle_3_deg15.274
r_scangle_it9.959
r_scbond_it6.941
r_dihedral_angle_1_deg5.745
r_mcangle_it3.509
r_mcbond_it2.722
r_angle_refined_deg1.957
r_nbtor_refined0.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.517
r_dihedral_angle_4_deg28.651
r_dihedral_angle_3_deg15.274
r_scangle_it9.959
r_scbond_it6.941
r_dihedral_angle_1_deg5.745
r_mcangle_it3.509
r_mcbond_it2.722
r_angle_refined_deg1.957
r_nbtor_refined0.325
r_symmetry_vdw_refined0.261
r_nbd_refined0.228
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.17
r_chiral_restr0.118
r_metal_ion_refined0.099
r_bond_refined_d0.018
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms831
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing