2HMF

Structure of a Threonine Sensitive Aspartokinase from Methanococcus jannaschii Complexed with Mg-ADP and Aspartate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293100 mM Tris pH 8.5 800 mM ammonium formate 13% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5151.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.741α = 90
b = 104.508β = 90
c = 192.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1APS14-ID-B

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
12.55084.60.04618.4608006080022
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)
2.52.59370.2772612

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT2CDQ2.75026080053864272794.120.2430.2410.276RANDOM47.452
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]
-3.17-0.964.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.037
r_dihedral_angle_3_deg18.294
r_dihedral_angle_4_deg17.236
r_dihedral_angle_1_deg5.453
r_scangle_it1.665
r_angle_refined_deg1.222
r_scbond_it0.948
r_mcangle_it0.791
r_mcbond_it0.472
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.037
r_dihedral_angle_3_deg18.294
r_dihedral_angle_4_deg17.236
r_dihedral_angle_1_deg5.453
r_scangle_it1.665
r_angle_refined_deg1.222
r_scbond_it0.948
r_mcangle_it0.791
r_mcbond_it0.472
r_nbtor_refined0.303
r_symmetry_vdw_refined0.294
r_symmetry_hbond_refined0.261
r_nbd_refined0.209
r_xyhbond_nbd_refined0.133
r_chiral_restr0.087
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14160
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms148

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing