3SI2

Structure of glycosylated murine glutaminyl cyclase in presence of the inhibitor PQ50 (PDBD150)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SI1PDB ENTRY 3SI1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.3294100 mM sodium acetate, 200 mM ammonium sulfate, 12% w/v PEG2000 MME, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.76α = 90
b = 83.06β = 90
c = 95.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252008-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.83099.80.10713.35.731637315763-325.495
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)
11.81.999.90.8192.33

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3SI11.819.05315743157415791000.18810.18810.18440.2597RANDOM21.3925
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]
-0.03-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.695
r_dihedral_angle_4_deg16.486
r_dihedral_angle_3_deg13.107
r_dihedral_angle_1_deg6.143
r_scangle_it4.915
r_scbond_it3.344
r_angle_refined_deg2.224
r_mcangle_it2.011
r_mcbond_it1.214
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.695
r_dihedral_angle_4_deg16.486
r_dihedral_angle_3_deg13.107
r_dihedral_angle_1_deg6.143
r_scangle_it4.915
r_scbond_it3.344
r_angle_refined_deg2.224
r_mcangle_it2.011
r_mcbond_it1.214
r_chiral_restr0.129
r_bond_refined_d0.022
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2622
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms74

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction