6HS9

The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529310% PEG 8000, 0.1M CaCl2, 0.1M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6954.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.55α = 90
b = 79.55β = 90
c = 72.28γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.826560DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.0532.0499.50.0540.0470.0280.99813.94.811995912.298
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.051.0798.80.7170.9140.5590.4771.42.4

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 REPLACEMENTTHROUGHOUT1GQO1.053274983406299.260.11390.11280.134RANDOM21.112
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]
-0.21-0.1-0.210.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.998
r_dihedral_angle_4_deg26.117
r_sphericity_free24.668
r_dihedral_angle_3_deg13.488
r_sphericity_bonded12.956
r_dihedral_angle_1_deg5.862
r_rigid_bond_restr5.076
r_angle_refined_deg2.051
r_angle_other_deg0.712
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.998
r_dihedral_angle_4_deg26.117
r_sphericity_free24.668
r_dihedral_angle_3_deg13.488
r_sphericity_bonded12.956
r_dihedral_angle_1_deg5.862
r_rigid_bond_restr5.076
r_angle_refined_deg2.051
r_angle_other_deg0.712
r_chiral_restr0.129
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1150
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms19

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction