7D2J

Crystal structure of Ixodes scapularis glutaminyl cyclase with a Cd ion 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) PEG 8000, 8%(v/v) ethylene glycol, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.1141.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.127α = 90
b = 71.936β = 90
c = 80.186γ = 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
11.63099.30.07527.35.642574
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)
11.61.6698.70.7582.75.3

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 REPLACEMENTTHROUGHOUT4MHN1.622.9840382214599.20.1710.16970.1965RANDOM19.354
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]
0.250.5-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.039
r_dihedral_angle_4_deg14.9
r_dihedral_angle_3_deg12.949
r_dihedral_angle_1_deg5.348
r_angle_refined_deg1.266
r_angle_other_deg0.748
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.039
r_dihedral_angle_4_deg14.9
r_dihedral_angle_3_deg12.949
r_dihedral_angle_1_deg5.348
r_angle_refined_deg1.266
r_angle_other_deg0.748
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms366
Heterogen Atoms5

Software

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