2QA2

Crystal structure of CabE, an aromatic hydroxylase from angucycline biosynthesis, determined to 2.7 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QA1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320 % PEG 3350, 0.1M bis-tris propane, 0.2M Na/K-phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9869.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.1α = 90
b = 133.1β = 90
c = 166.8γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
12.73099.10.0970.09716.226.8243792437950.7
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)
12.72.899.90.5180.51846.92467

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 REPLACEMENTTHROUGHOUT2QA12.729.832319023190122099.40.236330.236330.234280.27428RANDOM72.281
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]
-2.71-1.35-2.714.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.661
r_dihedral_angle_3_deg20.136
r_dihedral_angle_4_deg18.525
r_dihedral_angle_1_deg6.596
r_scangle_it1.607
r_angle_refined_deg1.403
r_mcangle_it1.321
r_scbond_it1.034
r_mcbond_it0.768
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.661
r_dihedral_angle_3_deg20.136
r_dihedral_angle_4_deg18.525
r_dihedral_angle_1_deg6.596
r_scangle_it1.607
r_angle_refined_deg1.403
r_mcangle_it1.321
r_scbond_it1.034
r_mcbond_it0.768
r_nbtor_refined0.313
r_symmetry_vdw_refined0.238
r_nbd_refined0.232
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.155
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.004
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_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms3675
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms53

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling