2CJE

THE CRYSTAL STRUCTURE OF A COMPLEX OF Leishmania major DUTPASE WITH SUBSTRATE ANALOGUE DUPNHP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OGKPDB ENTRY 1OGK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.530% PEG 3350 MME, 0.2 M MGCL2, 0.1M BIS-TRIS PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.866α = 90
b = 87.866β = 90
c = 146.531γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.343099.90.072813.8147133
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)
12.342.4299.90.433.38

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 1OGK2.3476.031384973799.20.1870.1840.238RANDOM50.77
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.765
r_dihedral_angle_4_deg19.711
r_dihedral_angle_3_deg17.212
r_dihedral_angle_1_deg6.074
r_scangle_it2.509
r_scbond_it1.665
r_angle_refined_deg1.497
r_mcangle_it1.096
r_angle_other_deg0.939
r_mcbond_it0.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.765
r_dihedral_angle_4_deg19.711
r_dihedral_angle_3_deg17.212
r_dihedral_angle_1_deg6.074
r_scangle_it2.509
r_scbond_it1.665
r_angle_refined_deg1.497
r_mcangle_it1.096
r_angle_other_deg0.939
r_mcbond_it0.669
r_symmetry_vdw_other0.294
r_nbd_refined0.218
r_nbtor_refined0.185
r_nbd_other0.178
r_xyhbond_nbd_refined0.17
r_mcbond_other0.14
r_symmetry_hbond_refined0.128
r_chiral_restr0.096
r_symmetry_vdw_refined0.092
r_nbtor_other0.085
r_bond_refined_d0.015
r_metal_ion_refined0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms2000
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing