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Engineered beta-lactoglobulin: variant L58F in complex with myristic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 2.80 M (NH4)2SO4 in 0.1 M Tris-HCl pH 8.0, 5 mM myristic acid
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.078 α = 90 b = 53.078 β = 90 c = 111.556 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD AGILENT ATLAS CCD 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.1 15.18 99.3 0.059 0.072 0.04 0.997 10.6 2.9 11062
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17 98.9 0.355 0.473 0.31 0.761 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BSY 2.1 14.78 9915 1124 98.92 0.19961 0.19439 0.24464 0.227 RANDOM 29.32
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] 0.01 0.01 0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.206 r_dihedral_angle_4_deg 22.461 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_1_deg 7.004 r_long_range_B_refined 4.463 r_long_range_B_other 4.293 r_scangle_other 1.55 r_angle_refined_deg 1.547 r_mcangle_it 1.282 r_mcangle_other 1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.206 r_dihedral_angle_4_deg 22.461 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_1_deg 7.004 r_long_range_B_refined 4.463 r_long_range_B_other 4.293 r_scangle_other 1.55 r_angle_refined_deg 1.547 r_mcangle_it 1.282 r_mcangle_other 1.281 r_angle_other_deg 1.21 r_scbond_it 0.999 r_scbond_other 0.963 r_mcbond_it 0.775 r_mcbond_other 0.774 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1160 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing