2VP5

Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J90PDB ENTRY 1J90

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.7948.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.616α = 90
b = 62.55β = 90
c = 68.205γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.35098.50.0713.13.4220452
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3291.20.372.12.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1J902.35022043119598.30.2360.2340.273RANDOM39.23
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]
-3.391.651.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.003
r_dihedral_angle_3_deg16.117
r_dihedral_angle_4_deg15.682
r_dihedral_angle_1_deg5.566
r_scangle_it2.386
r_scbond_it1.475
r_mcangle_it1.203
r_angle_refined_deg1.151
r_mcbond_it0.686
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.003
r_dihedral_angle_3_deg16.117
r_dihedral_angle_4_deg15.682
r_dihedral_angle_1_deg5.566
r_scangle_it2.386
r_scbond_it1.475
r_mcangle_it1.203
r_angle_refined_deg1.151
r_mcbond_it0.686
r_nbtor_refined0.305
r_symmetry_vdw_refined0.234
r_symmetry_hbond_refined0.193
r_nbd_refined0.185
r_xyhbond_nbd_refined0.149
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.003
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_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3135
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing