3GGL

X-Ray Structure of the C-terminal domain (277-440) of Putative chitobiase from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR324A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F2Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.75M MgFormate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9658.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.86α = 90
b = 86.86β = 90
c = 50.992γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2009-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.979NSLSX4A

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
135099.90.0859.48624-3
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)
33.111000.4848.6

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 REPLACEMENTTHROUGHOUT3F2Z32046152101000.2020.20.251RANDOM66.961
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]
-0.16-0.08-0.160.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.433
r_dihedral_angle_3_deg19.331
r_dihedral_angle_4_deg15.843
r_dihedral_angle_1_deg6.632
r_angle_refined_deg1.384
r_scangle_it1.142
r_scbond_it0.653
r_mcangle_it0.506
r_nbtor_refined0.324
r_mcbond_it0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.433
r_dihedral_angle_3_deg19.331
r_dihedral_angle_4_deg15.843
r_dihedral_angle_1_deg6.632
r_angle_refined_deg1.384
r_scangle_it1.142
r_scbond_it0.653
r_mcangle_it0.506
r_nbtor_refined0.324
r_mcbond_it0.304
r_symmetry_vdw_refined0.262
r_nbd_refined0.238
r_xyhbond_nbd_refined0.177
r_chiral_restr0.099
r_symmetry_hbond_refined0.027
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1243
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing