3R6O

Crystal structure of a probable 2-hydroxyhepta-2,4-diene-1, 7-dioateisomerase from Mycobacterium abscessus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7290EBS JCSG+ SCREEN B8: 200MM MGCL2, 100MM TRIS PH 7.0, 10% PEG 8000, MYABA.00471.B.A1 PS00908 AT 38.0MG/ML, CRYO PROTECTION: 25% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.3347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.68α = 90
b = 90.68β = 90
c = 76.13γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+RIGAKU VARIMAX HF2010-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.955099.90.0718.095.52252722511-329.55
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)
11.95299.90.5022.63.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3QDF1.9535.792252722475115999.70.1520.150.185RANDOM23.82
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]
-17.38-17.3834.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.472
r_dihedral_angle_3_deg14.446
r_dihedral_angle_4_deg13.836
r_dihedral_angle_1_deg6.601
r_scangle_it2.511
r_scbond_it1.55
r_angle_refined_deg1.499
r_angle_other_deg0.931
r_mcangle_it0.649
r_mcbond_it0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.472
r_dihedral_angle_3_deg14.446
r_dihedral_angle_4_deg13.836
r_dihedral_angle_1_deg6.601
r_scangle_it2.511
r_scbond_it1.55
r_angle_refined_deg1.499
r_angle_other_deg0.931
r_mcangle_it0.649
r_mcbond_it0.336
r_chiral_restr0.088
r_mcbond_other0.061
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1932
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms4

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling