3TPN

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
2.1442.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.333α = 90
b = 60.333β = 90
c = 64.519γ = 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
11.652097.90.0415.42.31580215802-3
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)
11.651.7598.30.4882.12.2

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 2D4L1.6518.88145641456482295.40.1590.1570.182RANDOM25.55
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_deg37.172
r_dihedral_angle_4_deg30.604
r_dihedral_angle_3_deg14.289
r_scangle_it8.905
r_dihedral_angle_1_deg6.075
r_scbond_it5.392
r_mcangle_it2.842
r_angle_refined_deg1.984
r_mcbond_it1.678
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.172
r_dihedral_angle_4_deg30.604
r_dihedral_angle_3_deg14.289
r_scangle_it8.905
r_dihedral_angle_1_deg6.075
r_scbond_it5.392
r_mcangle_it2.842
r_angle_refined_deg1.984
r_mcbond_it1.678
r_nbtor_refined0.322
r_nbd_refined0.239
r_symmetry_vdw_refined0.231
r_xyhbond_nbd_refined0.179
r_chiral_restr0.139
r_symmetry_hbond_refined0.106
r_metal_ion_refined0.049
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms830
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms45

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing