4S35

AMPPCP and TMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PBRpdb entry 2PBR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.42930.1 NaAcetate pH 5.4, 0.2 M MgFormate,10 mM dTMP, 10mM AMP-PCP, 10 mM MgCl2, 20% Glycerol as cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.479α = 90
b = 62.615β = 97.97
c = 73.577γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VRH Coated Bent-Cyrindrical MIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

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
11.555098.610.04733.597.13905135478113.4
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)
11.551.6190.40.1589.3765.35025

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 REPLACEMENTTHROUGHOUTpdb entry 2PBR1.555039051351970280998.60.147780.146320.17413RANDOM14.789
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]
-0.77-0.131.39-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.423
r_dihedral_angle_4_deg17.223
r_dihedral_angle_3_deg12.157
r_dihedral_angle_1_deg6.107
r_long_range_B_refined5.468
r_long_range_B_other5.265
r_scangle_other3.848
r_scbond_it2.568
r_scbond_other2.563
r_angle_refined_deg2.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.423
r_dihedral_angle_4_deg17.223
r_dihedral_angle_3_deg12.157
r_dihedral_angle_1_deg6.107
r_long_range_B_refined5.468
r_long_range_B_other5.265
r_scangle_other3.848
r_scbond_it2.568
r_scbond_other2.563
r_angle_refined_deg2.473
r_mcangle_it2.454
r_mcangle_other2.454
r_mcbond_it1.675
r_mcbond_other1.674
r_angle_other_deg1.026
r_chiral_restr0.145
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3071
Nucleic Acid Atoms
Solvent Atoms354
Heterogen Atoms117

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling