4F9V

Structure of C113A/C136A mutant variant of glycosylated glutaminyl cyclase from Drosophila melanogaster


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4F9UPDB ENTRY 4F9U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529412% PEG8000, 2 mM PQ50, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.4264.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.865α = 90
b = 170.865β = 90
c = 57.236γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225mirrors2010-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
12.1147.973980.1139.43.85522255179-3.727
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)
12.12.21990.6781.93.88055

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 4F9U2.1505522255179280798.450.1760.1760.1740.215RANDOM21.132
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]
-0.67-0.34-0.671.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.515
r_dihedral_angle_4_deg18.888
r_dihedral_angle_3_deg13.158
r_dihedral_angle_1_deg5.809
r_scangle_it3.311
r_scbond_it2.08
r_angle_refined_deg1.414
r_mcangle_it1.34
r_angle_other_deg0.901
r_mcbond_it0.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.515
r_dihedral_angle_4_deg18.888
r_dihedral_angle_3_deg13.158
r_dihedral_angle_1_deg5.809
r_scangle_it3.311
r_scbond_it2.08
r_angle_refined_deg1.414
r_mcangle_it1.34
r_angle_other_deg0.901
r_mcbond_it0.726
r_mcbond_other0.163
r_chiral_restr0.082
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4854
Nucleic Acid Atoms
Solvent Atoms685
Heterogen Atoms175

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling