3B6B

Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B8QPDB ENTRY 1B8Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529340-45% MPD, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.839α = 90
b = 152.528β = 90
c = 184.12γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.98025ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
127698.60.060.067.34.77279131.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1198.70.3030.3032.64.810642

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 1B8Q22070883375798.280.200580.199070.22894RANDOM33.532
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]
0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.467
r_dihedral_angle_4_deg20.477
r_dihedral_angle_3_deg15.23
r_dihedral_angle_1_deg5.999
r_scangle_it2.836
r_scbond_it1.673
r_angle_refined_deg1.305
r_mcangle_it1.223
r_mcbond_it0.699
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.467
r_dihedral_angle_4_deg20.477
r_dihedral_angle_3_deg15.23
r_dihedral_angle_1_deg5.999
r_scangle_it2.836
r_scbond_it1.673
r_angle_refined_deg1.305
r_mcangle_it1.223
r_mcbond_it0.699
r_nbtor_refined0.304
r_metal_ion_refined0.221
r_symmetry_vdw_refined0.213
r_nbd_refined0.199
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.131
r_chiral_restr0.1
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6303
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms168

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing