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Crystal Structure of Choline Oxidase in Complex with the Reaction Product Glycine Betaine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JBV PDB ENTRY 2JBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 mixing 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 coefficient Solvent content 2.63 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.35 α = 90 b = 87.35 β = 90 c = 353.484 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2012-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 43.35 97 0.098 14.2 4.5 97679 92704 19.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 89.3 0.428 3 3.6 8823
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2JBV 1.95 43.35 97679 92704 4869 96.94 0.1525 0.15099 0.1516 0.18106 0.1821 RANDOM 19.531
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 -0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 6.625 r_long_range_B_refined 5.855 r_scbond_it 3.154 r_angle_refined_deg 2.335 r_mcangle_it 1.868 r_mcbond_it 1.41 r_chiral_restr 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 6.625 r_long_range_B_refined 5.855 r_scbond_it 3.154 r_angle_refined_deg 2.335 r_mcangle_it 1.868 r_mcbond_it 1.41 r_chiral_restr 0.17 r_gen_planes_refined 0.02 r_bond_refined_d 0.016 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 Atoms Number Protein Atoms 8212 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 154
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling