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Crystal structure of human choline alpha in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 18-20% Peg-mme 5000, 0.1 M Magnesium Formate, 0.1 M HEPES pH 7.0.
Crystal Properties Matthews coefficient Solvent content 2.44 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.593 α = 90 b = 120.926 β = 90 c = 130.456 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 PIXEL DECTRIS EIGER2 XE 16M 2020-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 55.59 99.7 0.063 19 9.9 35130
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 2.49 99.9 0.689 9.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2CKQ 2.4 51.196 35071 1718 99.571 0.204 0.2017 0.2477 0.2155 62.682
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] -1.157 5.936 -4.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.525 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 17.302 r_lrange_it 10.784 r_scangle_it 8.583 r_mcangle_it 7.13 r_dihedral_angle_1_deg 6.395 r_scbond_it 6.228 r_mcbond_it 4.895 r_angle_refined_deg 1.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.525 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 17.302 r_lrange_it 10.784 r_scangle_it 8.583 r_mcangle_it 7.13 r_dihedral_angle_1_deg 6.395 r_scbond_it 6.228 r_mcbond_it 4.895 r_angle_refined_deg 1.389 r_nbtor_refined 0.316 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.176 r_symmetry_nbd_refined 0.166 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.106 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5702 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing