3I2H

Cocaine Esterase with mutation L169K, bound to DTT adduct


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JU3PDB: 1JU3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529310mM Tris pH 7.5, 25 mM NaCl, 1.6 M Ammonium Sulfate, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8156.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.438α = 90
b = 105.438β = 90
c = 222.188γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2006-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033APS23-ID-B

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
11.655099.90.059235.988021
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)
11.651.7199.60.64321.98610

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 DIFFRACTIONDifference fourierTHROUGHOUTPDB: 1JU31.6519.9887941440999.910.155030.155030.146RANDOM21.608
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]
-0.31-0.15-0.310.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.276
r_dihedral_angle_4_deg12.921
r_dihedral_angle_3_deg11.368
r_dihedral_angle_1_deg6.018
r_scangle_it1.945
r_scbond_it1.212
r_angle_refined_deg1.117
r_mcangle_it0.782
r_mcbond_it0.461
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.276
r_dihedral_angle_4_deg12.921
r_dihedral_angle_3_deg11.368
r_dihedral_angle_1_deg6.018
r_scangle_it1.945
r_scbond_it1.212
r_angle_refined_deg1.117
r_mcangle_it0.782
r_mcbond_it0.461
r_nbtor_refined0.304
r_nbd_refined0.217
r_symmetry_vdw_refined0.161
r_symmetry_hbond_refined0.123
r_xyhbond_nbd_refined0.098
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4384
Nucleic Acid Atoms
Solvent Atoms778
Heterogen Atoms53

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction