3PB7

Crystal structure of the catalytic domain of human Golgi-resident glutaminyl cyclase in complex with PBD150


X-RAY DIFFRACTION

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
1.9536.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.366α = 90
b = 69.917β = 90
c = 77.42γ = 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
11.43092.30.06336.97.6578975343933
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)
11.41.451000.5283.37.65713

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 REPLACEMENTTHROUGHOUT3PB41.4305482950547267892.190.159170.156730.20732RANDOM16.255
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]
0.45-0.540.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.629
r_dihedral_angle_4_deg22.795
r_dihedral_angle_3_deg13.289
r_scangle_it6.412
r_dihedral_angle_1_deg6.003
r_scbond_it4.627
r_mcangle_it3.117
r_rigid_bond_restr2.448
r_mcbond_it2.297
r_angle_refined_deg2.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.629
r_dihedral_angle_4_deg22.795
r_dihedral_angle_3_deg13.289
r_scangle_it6.412
r_dihedral_angle_1_deg6.003
r_scbond_it4.627
r_mcangle_it3.117
r_rigid_bond_restr2.448
r_mcbond_it2.297
r_angle_refined_deg2.039
r_chiral_restr0.132
r_bond_refined_d0.024
r_gen_planes_refined0.014
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 Atoms404
Heterogen Atoms23

Software

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