3WRB

Crystal structure of the anaerobic H124F DESb-Gallate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WR8DesB substrate-free form

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.7529325% PEG8000, 0.1M SODIUM ACETATE, 0.1M HEPES-NAOH, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.349α = 90
b = 65.519β = 96.93
c = 117.875γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702010-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A0.97951Photon FactoryAR-NE3A

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
12.158.598.80.0715.174.45095050339
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2198.76.944.16

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 REPLACEMENTTHROUGHOUTDesB substrate-free form2.158478914789125211000.1950.1950.1920.243RANDOM22.88
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]
0.70.071.09-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.265
r_dihedral_angle_4_deg18.123
r_dihedral_angle_3_deg13.407
r_dihedral_angle_1_deg5.636
r_scangle_it2.65
r_scbond_it1.624
r_angle_refined_deg1.21
r_mcangle_it0.959
r_mcbond_it0.506
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.265
r_dihedral_angle_4_deg18.123
r_dihedral_angle_3_deg13.407
r_dihedral_angle_1_deg5.636
r_scangle_it2.65
r_scbond_it1.624
r_angle_refined_deg1.21
r_mcangle_it0.959
r_mcbond_it0.506
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms6506
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms26

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling