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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 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.855 α = 90 b = 122.003 β = 90 c = 132.121 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 PILATUS 6M-F 2017-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
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 2.3 47.4 100 0.056 20.3 7.3 40989
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 2.3 2.42 100 0.659 3.3 7.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2CKQ 2.3 44.857 40925 2094 99.937 0.197 0.1946 0.1946 0.2486 0.2487 55.247
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] -0.612 3.361 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.028 r_dihedral_angle_4_deg 18.992 r_dihedral_angle_3_deg 16.92 r_lrange_it 10.917 r_scangle_it 8.847 r_dihedral_angle_1_deg 6.715 r_mcangle_it 6.584 r_scbond_it 6.185 r_mcbond_it 4.622 r_angle_refined_deg 1.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.028 r_dihedral_angle_4_deg 18.992 r_dihedral_angle_3_deg 16.92 r_lrange_it 10.917 r_scangle_it 8.847 r_dihedral_angle_1_deg 6.715 r_mcangle_it 6.584 r_scbond_it 6.185 r_mcbond_it 4.622 r_angle_refined_deg 1.422 r_nbtor_refined 0.317 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.143 r_chiral_restr 0.112 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5788 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing