3PB9

Crystal structure of the catalytic domain of human Golgi-resident glutaminyl cyclase in complex with 1-benzylimidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PB4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629330%(v/v) PEG 200, 5%(w/v) PEG 3000, 0.1M Mes, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9336.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.562α = 90
b = 69.202β = 90
c = 77.402γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

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
11.123096.90.05335.25.311112110767633
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)
11.121.16910.4162.22.910975

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 REPLACEMENTTHROUGHOUT3PB41.1230105419102035539396.790.151220.149610.18123RANDOM15.413
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]
0.49-0.23-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.425
r_dihedral_angle_4_deg23.983
r_dihedral_angle_3_deg12.013
r_dihedral_angle_1_deg6.327
r_scangle_it6.158
r_scbond_it4.499
r_mcangle_it3.308
r_rigid_bond_restr2.664
r_mcbond_it2.371
r_angle_refined_deg2.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.425
r_dihedral_angle_4_deg23.983
r_dihedral_angle_3_deg12.013
r_dihedral_angle_1_deg6.327
r_scangle_it6.158
r_scbond_it4.499
r_mcangle_it3.308
r_rigid_bond_restr2.664
r_mcbond_it2.371
r_angle_refined_deg2.268
r_chiral_restr0.136
r_bond_refined_d0.028
r_gen_planes_refined0.015
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2444
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms13

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling