3TPS

Crystal structure of M-PMV dUTPASE complexed with dUPNPP substrate


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
2.1241.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.708α = 90
b = 60.708β = 90
c = 64.363γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2005-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8430EMBL/DESY, HAMBURGBW7B

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
11.852098.60.0679.62.31140711407-3
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)
11.851.951000.5152.12.31682

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 2D4L1.8520113531074660798.520.17040.16910.1926RANDOM29.651
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]
1.070.531.07-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.38
r_dihedral_angle_4_deg30.488
r_dihedral_angle_3_deg14.744
r_dihedral_angle_1_deg12.924
r_scangle_it6.401
r_scbond_it5.001
r_mcangle_it3.147
r_angle_refined_deg2.035
r_mcbond_it1.95
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.38
r_dihedral_angle_4_deg30.488
r_dihedral_angle_3_deg14.744
r_dihedral_angle_1_deg12.924
r_scangle_it6.401
r_scbond_it5.001
r_mcangle_it3.147
r_angle_refined_deg2.035
r_mcbond_it1.95
r_nbtor_refined0.317
r_symmetry_vdw_refined0.259
r_nbd_refined0.237
r_xyhbond_nbd_refined0.184
r_chiral_restr0.135
r_symmetry_hbond_refined0.08
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms822
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms37

Software

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