3TL2

Crystal structure of Bacillus anthracis str. Ames malate dehydrogenase in closed conformation.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729320% w/v PEG 3350, 0.2M Na Thiocyanate, 2% w/v Hexandiol, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4349.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.181α = 90
b = 68.377β = 90
c = 142.919γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9772APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.75099.90.0760.07627.873697936979-315.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.73990.7090.7092.24.71832

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1uxj1.739.093380833808178097.070.159230.159230.157210.19764RANDOM16.578
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]
0.42-0.07-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.422
r_dihedral_angle_4_deg16.856
r_dihedral_angle_3_deg11.661
r_dihedral_angle_1_deg6.317
r_angle_refined_deg1.749
r_angle_other_deg1.032
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.422
r_dihedral_angle_4_deg16.856
r_dihedral_angle_3_deg11.661
r_dihedral_angle_1_deg6.317
r_angle_refined_deg1.749
r_angle_other_deg1.032
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2353
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms14

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling