3DKD

Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with GDP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529340-45% 2-Methyl-2,4-pentane-d12-diol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.07α = 90
b = 70.07β = 90
c = 103.221γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 210mirrors2007-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
11.9601000.1173.67.12263918.6
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)
1.921000.351.95.33288

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 REPLACEMENTTHROUGHOUT2B8Q1.93021485115999.990.182970.181220.21563RANDOM19.347
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]
-0.13-0.07-0.130.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.809
r_dihedral_angle_4_deg17.912
r_dihedral_angle_3_deg12.858
r_dihedral_angle_1_deg5.786
r_scangle_it2.179
r_scbond_it1.294
r_angle_refined_deg1.154
r_mcangle_it0.826
r_mcbond_it0.48
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.809
r_dihedral_angle_4_deg17.912
r_dihedral_angle_3_deg12.858
r_dihedral_angle_1_deg5.786
r_scangle_it2.179
r_scbond_it1.294
r_angle_refined_deg1.154
r_mcangle_it0.826
r_mcbond_it0.48
r_nbtor_refined0.299
r_symmetry_vdw_refined0.195
r_nbd_refined0.187
r_symmetry_hbond_refined0.149
r_xyhbond_nbd_refined0.124
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2112
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing