3EE3

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429340 to 44% MPD, 0.1M MOPS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0459.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.419α = 90
b = 154.419β = 90
c = 187.039γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315mirrors2007-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.064ESRFID29

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
12.495.399.70.07764.7454814548156.3
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)
2.42.5399.90.4331.74.86609

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.42044357236699.590.196350.19440.23347RANDOM47.789
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]
0.08-0.120.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_4_deg25.698
r_dihedral_angle_3_deg17.887
r_dihedral_angle_1_deg6.761
r_scangle_it3.018
r_scbond_it1.857
r_angle_refined_deg1.542
r_mcangle_it1.309
r_mcbond_it0.732
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_4_deg25.698
r_dihedral_angle_3_deg17.887
r_dihedral_angle_1_deg6.761
r_scangle_it3.018
r_scbond_it1.857
r_angle_refined_deg1.542
r_mcangle_it1.309
r_mcbond_it0.732
r_nbtor_refined0.299
r_symmetry_vdw_refined0.222
r_nbd_refined0.208
r_symmetry_hbond_refined0.177
r_xyhbond_nbd_refined0.147
r_chiral_restr0.1
r_metal_ion_refined0.078
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6312
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms156

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling