3TQ4

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
2.141.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.564α = 90
b = 60.564β = 90
c = 64.018γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2004-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8028, 1.0720EMBL/DESY, HAMBURGX11

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
11.652.4197.60.07213.33.81723417234-3
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)
11.61.69970.4032.932584

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 DIFFRACTIONrigid body refinementTHROUGHOUTPDB entry 2D4L1.620172341630592997.610.17320.17220.191RANDOM25.406
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]
0.990.490.99-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.387
r_dihedral_angle_4_deg26.211
r_dihedral_angle_3_deg13.54
r_dihedral_angle_1_deg6.031
r_scangle_it5.321
r_scbond_it4.261
r_mcangle_it2.878
r_angle_refined_deg1.952
r_mcbond_it1.502
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.387
r_dihedral_angle_4_deg26.211
r_dihedral_angle_3_deg13.54
r_dihedral_angle_1_deg6.031
r_scangle_it5.321
r_scbond_it4.261
r_mcangle_it2.878
r_angle_refined_deg1.952
r_mcbond_it1.502
r_nbtor_refined0.314
r_symmetry_hbond_refined0.235
r_nbd_refined0.229
r_symmetry_vdw_refined0.229
r_xyhbond_nbd_refined0.185
r_symmetry_metal_ion_refined0.167
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms815
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing