2ZYQ

Crystal structure of the HsaC extradiol dioxygenase from M. tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.8298pH 6.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0459.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.737α = 90
b = 123.737β = 90
c = 106.784γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.541

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
122699.90.0940.0917.7145659756445121.5
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)
22.299.90.4580.4411.613.4

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 1KND220535925353628611000.180.1820.180.223RANDOM19.41
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]
-0.53-0.531.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.827
r_dihedral_angle_4_deg17.957
r_dihedral_angle_3_deg16.146
r_dihedral_angle_1_deg10.497
r_angle_refined_deg1.673
r_mcangle_it1.344
r_mcbond_it0.893
r_nbtor_refined0.298
r_nbd_refined0.207
r_symmetry_vdw_refined0.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.827
r_dihedral_angle_4_deg17.957
r_dihedral_angle_3_deg16.146
r_dihedral_angle_1_deg10.497
r_angle_refined_deg1.673
r_mcangle_it1.344
r_mcbond_it0.893
r_nbtor_refined0.298
r_nbd_refined0.207
r_symmetry_vdw_refined0.197
r_xyhbond_nbd_refined0.176
r_symmetry_hbond_refined0.169
r_chiral_restr0.132
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4677
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms12

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling