7D1D

Crystal structure of Bacteroides thetaiotaomicron glutaminyl cyclase bound to 1-benzylimidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FUU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293.150.2 M NaCl, 0.1 M Bis-Tris, pH 5.5, 25% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1141.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.302α = 90
b = 78.536β = 114.51
c = 49.221γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2019-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

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
11.754599.90.06515.93.328784
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)
11.751.8199.60.52623.1

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 REPLACEMENTTHROUGHOUT4FUU1.7544.7926707144797.720.13520.13290.1795RANDOM22.831
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]
-0.060.04-0.170.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.472
r_dihedral_angle_4_deg22.509
r_sphericity_free20.684
r_dihedral_angle_3_deg14.486
r_dihedral_angle_1_deg5.708
r_sphericity_bonded5.238
r_angle_refined_deg1.315
r_rigid_bond_restr1.162
r_angle_other_deg0.909
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.472
r_dihedral_angle_4_deg22.509
r_sphericity_free20.684
r_dihedral_angle_3_deg14.486
r_dihedral_angle_1_deg5.708
r_sphericity_bonded5.238
r_angle_refined_deg1.315
r_rigid_bond_restr1.162
r_angle_other_deg0.909
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2333
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms13

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction