3P7M

Structure of putative lactate dehydrogenase from Francisella tularensis subsp. tularensis SCHU S4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GVHPDB entry 3GVH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.2M NH4 dihydrogen Phosphate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.74α = 90
b = 99.147β = 103.54
c = 83.345γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2009-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9791APS19-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
12.25099.20.1260.12614.94.16212862128-331.2
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)
2.22.241000.4970.4972.734.13136

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 3GVH2.2505481154811296491.390.184680.184680.182040.23307RANDOM27.599
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]
0.14-0.72-0.33-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.447
r_dihedral_angle_4_deg17.646
r_dihedral_angle_3_deg16.008
r_dihedral_angle_1_deg5.228
r_angle_other_deg4.332
r_scangle_it3.942
r_scbond_it2.896
r_angle_refined_deg1.6
r_mcangle_it1.157
r_mcbond_it0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.447
r_dihedral_angle_4_deg17.646
r_dihedral_angle_3_deg16.008
r_dihedral_angle_1_deg5.228
r_angle_other_deg4.332
r_scangle_it3.942
r_scbond_it2.896
r_angle_refined_deg1.6
r_mcangle_it1.157
r_mcbond_it0.66
r_chiral_restr0.095
r_bond_refined_d0.021
r_gen_planes_other0.012
r_gen_planes_refined0.007
r_bond_other_d
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9367
Nucleic Acid Atoms
Solvent Atoms538
Heterogen Atoms10

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling