4MJW

Crystal Structure of Choline Oxidase in Complex with the Reaction Product Glycine Betaine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JBVPDB ENTRY 2JBV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298mixing 1 uL of choline oxidase (6.6 mg/mL) with 1 uL of reservoir solution containing 0.1 M magnesium acetate, pH 6.0, 50 mM calcium chloride, 2.5% v/v glycerol, and 10% w/v PEG 6000 (reservoir 500 uL), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6352.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.35α = 90
b = 87.35β = 90
c = 353.484γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
11.9543.35970.09814.24.5976799270419.8
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)
11.952.0289.30.42833.68823

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JBV1.9543.359767992704486996.940.15250.150990.18106RANDOM19.531
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]
-0.04-0.040.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.36
r_dihedral_angle_4_deg18.55
r_dihedral_angle_3_deg13.669
r_dihedral_angle_1_deg6.625
r_long_range_B_refined5.855
r_scbond_it3.154
r_angle_refined_deg2.335
r_mcangle_it1.868
r_mcbond_it1.41
r_chiral_restr0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.36
r_dihedral_angle_4_deg18.55
r_dihedral_angle_3_deg13.669
r_dihedral_angle_1_deg6.625
r_long_range_B_refined5.855
r_scbond_it3.154
r_angle_refined_deg2.335
r_mcangle_it1.868
r_mcbond_it1.41
r_chiral_restr0.17
r_gen_planes_refined0.02
r_bond_refined_d0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms8212
Nucleic Acid Atoms
Solvent Atoms734
Heterogen Atoms154

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling