3EIC

X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with UDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B8Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4273MPD 40 to 44%, MOPS 0.1M, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.957.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.472α = 90
b = 152.726β = 90
c = 184.94γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315mirrors2007-07-23MSINGLE 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
12.392.499.70.071654955747.885
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)
2.32.421000.3312.35.17285

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2b8q2.3204810948109257099.620.189970.188140.22437RANDOM42.298
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]
-0.030.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.054
r_dihedral_angle_4_deg24.046
r_dihedral_angle_3_deg17.528
r_dihedral_angle_1_deg6.398
r_scangle_it3.293
r_scbond_it1.965
r_angle_refined_deg1.396
r_mcangle_it1.315
r_mcbond_it0.723
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.054
r_dihedral_angle_4_deg24.046
r_dihedral_angle_3_deg17.528
r_dihedral_angle_1_deg6.398
r_scangle_it3.293
r_scbond_it1.965
r_angle_refined_deg1.396
r_mcangle_it1.315
r_mcbond_it0.723
r_nbtor_refined0.304
r_nbd_refined0.213
r_symmetry_vdw_refined0.208
r_xyhbond_nbd_refined0.145
r_chiral_restr0.096
r_symmetry_hbond_refined0.08
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6338
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms156

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling