5A7H

Comparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A7FPDB ENTRY 5A7F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5277CRYSTALS WERE GROWN AT 4C IN 0.1 M BIS-TRIS PROPANE, PH 7.5, CONTAINING 20 % (W/V) POLYETHYLENE GLYCOL 3350, 0.2 M NAI
Crystal Properties
Matthews coefficientSolvent content
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.47α = 90
b = 115.47β = 90
c = 127.28γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.0178.6398.30.069.7341414
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)
12.012.06980.611.33

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5A7F2.0130.3438317203495.730.181230.178970.22163RANDOM43.37
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]
0.030.030.03-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.668
r_dihedral_angle_4_deg16.138
r_dihedral_angle_3_deg14.513
r_dihedral_angle_1_deg5.914
r_scangle_it5.477
r_mcangle_it3.865
r_scbond_it2.912
r_mcbond_it2.72
r_mcbond_other2.719
r_angle_refined_deg1.469
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.668
r_dihedral_angle_4_deg16.138
r_dihedral_angle_3_deg14.513
r_dihedral_angle_1_deg5.914
r_scangle_it5.477
r_mcangle_it3.865
r_scbond_it2.912
r_mcbond_it2.72
r_mcbond_other2.719
r_angle_refined_deg1.469
r_angle_other_deg0.784
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4125
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing