2D4N

Crystal Structure of M-PMV dUTPase complexed with dUPNPP, substrate analogue


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 8000, AMMONIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.1442.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.071α = 90
b = 61.071β = 90
c = 64.357γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8128EMBL/DESY, HAMBURGX11

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
11.5252.9398.720.0760.05712.342.662078720787-325
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)
11.521.6198.230.4420.3342.862.133282

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 DIFFRACTIONrigid body refinementTHROUGHOUT2D4L1.53201929619296109798.970.165660.165660.164430.18717from starting model22.778
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]
0.610.30.61-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.353
r_dihedral_angle_4_deg30.573
r_dihedral_angle_3_deg11.11
r_scangle_it10.457
r_scbond_it8.097
r_dihedral_angle_1_deg5.752
r_mcangle_it3.883
r_mcbond_it2.624
r_angle_refined_deg1.911
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.353
r_dihedral_angle_4_deg30.573
r_dihedral_angle_3_deg11.11
r_scangle_it10.457
r_scbond_it8.097
r_dihedral_angle_1_deg5.752
r_mcangle_it3.883
r_mcbond_it2.624
r_angle_refined_deg1.911
r_nbtor_refined0.315
r_nbd_refined0.235
r_xyhbond_nbd_refined0.218
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.172
r_chiral_restr0.141
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_metal_ion_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms826
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling