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Engineered beta-lactoglobulin: variant I56F
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 2.60 M (NH4)2SO4 in 0.1 M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.272 α = 90 b = 53.272 β = 90 c = 113.051 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 2015-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.5406
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 13.81 98.5 0.088 0.11 0.065 0.993 7.4 2.5 12897
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 2.05 96.4 0.446 0.606 0.407 0.596 1.7 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 1BSY 2 13.81 11587 1308 98.08 0.2136 0.2074 0.2157 0.2687 0.2738 RANDOM 28.2
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 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 1242 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing