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Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in a closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X90 Homology Model based on LPLA2 (4x90) generated by MODELLER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.2 M ammonium formate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.52 65.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.887 α = 90 b = 123.532 β = 96.19 c = 114.778 γ = 90
Symmetry Space Group P 1 21 1
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 2014-04-17 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97919 APS 21-ID-D 2 SYNCHROTRON APS BEAMLINE 23-ID-D 0.984 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3.1 48.3 99.6 0.176 0.99 6.6 4.1 48188
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 98.3 1.262 0.577 1.1 4.2
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 Homology Model based on LPLA2 (4x90) generated by MODELLER 3.1 20 45564 2365 99.02 0.2504 0.24955 0.2587 0.26651 0.276 RANDOM 88.889
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] 3.93 6.77 -5.37 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.526 r_dihedral_angle_3_deg 13.873 r_dihedral_angle_4_deg 13.03 r_long_range_B_refined 6.504 r_long_range_B_other 6.504 r_dihedral_angle_1_deg 5.921 r_mcangle_other 4.023 r_mcangle_it 4.022 r_scangle_other 3.549 r_mcbond_it 2.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.526 r_dihedral_angle_3_deg 13.873 r_dihedral_angle_4_deg 13.03 r_long_range_B_refined 6.504 r_long_range_B_other 6.504 r_dihedral_angle_1_deg 5.921 r_mcangle_other 4.023 r_mcangle_it 4.022 r_scangle_other 3.549 r_mcbond_it 2.295 r_mcbond_other 2.293 r_scbond_it 1.986 r_scbond_other 1.985 r_angle_refined_deg 1.318 r_angle_other_deg 1.042 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12156 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement XDS data scaling Aimless data scaling PHASER phasing