3TPW

CRYSTAL STRUCTURE OF M-PMV DUTPASE - DUPNPP complex revealing distorted ligand geometry (approach intermediate)


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
2.0941.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.619α = 90
b = 60.619β = 90
c = 63.731γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmBENT, VERTICALLY FOCUSING MIRROR2005-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8034EMBL/DESY, HAMBURGX13

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
11.652098.40.056212.91582715827-3
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)
11.651.7399.20.2624.32.52107

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 2D4L1.6520158261497385398.440.16830.16680.1945RANDOM26.6316
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]
0.670.340.67-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.366
r_dihedral_angle_4_deg27.458
r_dihedral_angle_3_deg11.317
r_scangle_it8.845
r_scbond_it6.526
r_dihedral_angle_1_deg6.206
r_mcangle_it5.223
r_mcbond_it4.827
r_angle_refined_deg2.196
r_nbtor_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.366
r_dihedral_angle_4_deg27.458
r_dihedral_angle_3_deg11.317
r_scangle_it8.845
r_scbond_it6.526
r_dihedral_angle_1_deg6.206
r_mcangle_it5.223
r_mcbond_it4.827
r_angle_refined_deg2.196
r_nbtor_refined0.327
r_symmetry_vdw_refined0.24
r_nbd_refined0.239
r_symmetry_hbond_refined0.219
r_xyhbond_nbd_refined0.171
r_chiral_restr0.128
r_metal_ion_refined0.026
r_bond_refined_d0.018
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms828
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms37

Software

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