7D1P

Crystal structure of Ixodes scapularis glutaminyl cyclase with three Cd ions bound to the active site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.1510%(w/v) PEG8000, 8%(v/v) ethylene glycol, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0840.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.516α = 90
b = 73.766β = 90
c = 84.421γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

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
12.363098.60.11610.64.513295
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)
12.362.4490.60.4362.13.6

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 REPLACEMENTTHROUGHOUT4MHN2.3625.271221462695.370.18660.18260.2677RANDOM34.356
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]
0.180.1-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.488
r_dihedral_angle_3_deg17.015
r_dihedral_angle_4_deg15.441
r_dihedral_angle_1_deg7.267
r_angle_refined_deg1.62
r_angle_other_deg0.837
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.488
r_dihedral_angle_3_deg17.015
r_dihedral_angle_4_deg15.441
r_dihedral_angle_1_deg7.267
r_angle_refined_deg1.62
r_angle_other_deg0.837
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2665
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms13

Software

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