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Crystal structure of human LCAT (L4F, N5D) in complex with Fab of an agonistic antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M Hepes pH 7, 5% PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.29 62.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.944 α = 90 b = 127.595 β = 90 c = 256.079 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 ADSC QUANTUM 315r 2011-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.45 29.88 93.5 0.114 0.048 0.997 12.2 5.7 66187 44.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 85.1 1.268 0.521 0.612 1.6 5.7 3819
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4XWG 2.45 29.88 1.34 66114 3224 93.25 0.1911 0.1885 0.1949 0.2415 0.2449 Random selection 53.133
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.899 f_angle_d 1.306 f_chiral_restr 0.048 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9536 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 111
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing MOSFLM data reduction Aimless data scaling