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Engineered beta-lactoglobulin: variant L58F
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 293 2.80 M (NH4)2SO4 in 0.1 M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.45 49.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.674 α = 90 b = 52.674 β = 90 c = 112.013 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 2014-11-25 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 2.2 15.23 98.3 0.085 0.103 0.057 0.99 6.8 2.8 9457
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 2.2 2.27 93.9 0.183 0.254 0.176 0.878 2.3 1.8
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 1BSY 2.2 13.68 8651 782 97.92 0.1907 0.1851 0.1936 0.2514 0.2593 RANDOM 25.017
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] -0.03 -0.01 -0.03 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_3_deg 17.318 r_dihedral_angle_4_deg 15.967 r_dihedral_angle_1_deg 7.174 r_long_range_B_refined 6.258 r_long_range_B_other 6.179 r_scangle_other 3.758 r_mcangle_it 3.03 r_mcangle_other 3.028 r_scbond_it 2.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_3_deg 17.318 r_dihedral_angle_4_deg 15.967 r_dihedral_angle_1_deg 7.174 r_long_range_B_refined 6.258 r_long_range_B_other 6.179 r_scangle_other 3.758 r_mcangle_it 3.03 r_mcangle_other 3.028 r_scbond_it 2.279 r_scbond_other 2.279 r_mcbond_it 1.897 r_mcbond_other 1.896 r_angle_refined_deg 1.362 r_angle_other_deg 0.772 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 1234 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing