2WZT

Crystal structure of a mycobacterium aldo-keto reductase in its apo and liganded form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VBJPDB ENTRY 1VBJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.120% PEG 0.2M CACL2 0.1M NA CACODYLATE PH 5.1
Crystal Properties
Matthews coefficientSolvent content
2.244.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.543α = 90
b = 103.677β = 90
c = 112.051γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKE2006-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.926.31000.079.34.4408962
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)
11.921000.332.34.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1VBJ1.95038786204799.950.170050.167960.20941RANDOM14.078
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]
-1.01-1.162.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.134
r_dihedral_angle_4_deg13.665
r_dihedral_angle_3_deg13.607
r_dihedral_angle_1_deg5.68
r_scangle_it4.635
r_scbond_it3.392
r_mcangle_it2.024
r_mcbond_it1.389
r_angle_refined_deg1.348
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.134
r_dihedral_angle_4_deg13.665
r_dihedral_angle_3_deg13.607
r_dihedral_angle_1_deg5.68
r_scangle_it4.635
r_scbond_it3.392
r_mcangle_it2.024
r_mcbond_it1.389
r_angle_refined_deg1.348
r_nbtor_refined0.295
r_symmetry_metal_ion_refined0.231
r_symmetry_vdw_refined0.202
r_nbd_refined0.199
r_metal_ion_refined0.182
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.115
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3847
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing