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Structure of CutC choline lyase choline bound form from Klebsiella pneumoniae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9D PDB ENTRY 1R9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 20% PEG 3350, 60-20 MM K/NA TARTRATE, 100 MM BIS-TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.41 α = 90 b = 221.87 β = 90 c = 419.48 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MIRRORS 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 2.4 209.74 93.6 0.17 4.7 3 289262 2
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 2.4 2.46 87.8 0.512 1.8 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1R9D 2.4 209.74 289262 15197 93.57 0.19083 0.18787 0.1938 0.24699 0.249 RANDOM 28.181
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] 1.15 -1.62 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.359 r_dihedral_angle_4_deg 19.405 r_dihedral_angle_3_deg 18.342 r_dihedral_angle_1_deg 6.744 r_scangle_it 2.688 r_mcangle_it 2.297 r_scbond_it 1.647 r_angle_refined_deg 1.565 r_mcbond_it 1.448 r_mcbond_other 1.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.359 r_dihedral_angle_4_deg 19.405 r_dihedral_angle_3_deg 18.342 r_dihedral_angle_1_deg 6.744 r_scangle_it 2.688 r_mcangle_it 2.297 r_scbond_it 1.647 r_angle_refined_deg 1.565 r_mcbond_it 1.448 r_mcbond_other 1.448 r_angle_other_deg 0.878 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 50095 Nucleic Acid Atoms Solvent Atoms 1976 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing