7WP3

Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from Leishmania donovani with 1,5-Bis (4-amidinophenoxy) pentane (PNT) at 2.95 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529820% PEG 3350, 200mM sodium malonate
Crystal Properties
Matthews coefficientSolvent content
4.3871.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.024α = 90
b = 150.664β = 90
c = 170.547γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2015-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
12.9543.4998.80.1211.64.972691
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)
12.953.0384.520.491

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5B7O2.95443.48572691143798.8070.2120.2110.256790.593
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]
0.1360.044-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.76
r_lrange_it19.41
r_lrange_other19.41
r_scangle_it14.274
r_scangle_other14.274
r_dihedral_angle_3_deg12.375
r_mcangle_it11.062
r_mcangle_other11.062
r_dihedral_angle_4_deg10.342
r_scbond_it9.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.76
r_lrange_it19.41
r_lrange_other19.41
r_scangle_it14.274
r_scangle_other14.274
r_dihedral_angle_3_deg12.375
r_mcangle_it11.062
r_mcangle_other11.062
r_dihedral_angle_4_deg10.342
r_scbond_it9.336
r_scbond_other9.33
r_mcbond_other7.425
r_mcbond_it7.424
r_dihedral_angle_1_deg5.864
r_angle_other_deg2.291
r_dihedral_angle_other_2_deg1.815
r_angle_refined_deg1.31
r_nbd_other0.505
r_symmetry_nbd_refined0.468
r_symmetry_xyhbond_nbd_refined0.359
r_symmetry_nbd_other0.231
r_nbd_refined0.218
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.133
r_symmetry_xyhbond_nbd_other0.078
r_symmetry_nbtor_other0.068
r_chiral_restr0.05
r_bond_other_d0.035
r_bond_refined_d0.007
r_gen_planes_other0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11514
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing