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Engineered beta-lactoglobulin: variant M107L 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 293 1.34 M tri-sodium citrate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.182 α = 90 b = 53.182 β = 90 c = 112.285 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 2014-12-18 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 14.2 99.1 0.057 0.071 0.041 0.998 10.9 2.6 11138
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 2.16 97.2 0.446 0.616 0.422 0.651 1.9
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 2.1 13.47 9974 1138 98.61 0.1788 0.1739 0.1864 0.2213 0.2269 RANDOM 35.314
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] -0.07 -0.03 -0.07 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.513 r_dihedral_angle_4_deg 20.083 r_dihedral_angle_3_deg 16.488 r_long_range_B_refined 7.875 r_long_range_B_other 7.829 r_dihedral_angle_1_deg 7.124 r_scangle_other 6.161 r_scbond_it 4.419 r_scbond_other 4.416 r_mcangle_it 3.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.513 r_dihedral_angle_4_deg 20.083 r_dihedral_angle_3_deg 16.488 r_long_range_B_refined 7.875 r_long_range_B_other 7.829 r_dihedral_angle_1_deg 7.124 r_scangle_other 6.161 r_scbond_it 4.419 r_scbond_other 4.416 r_mcangle_it 3.197 r_mcangle_other 3.195 r_mcbond_it 2.513 r_mcbond_other 2.512 r_angle_refined_deg 1.315 r_angle_other_deg 0.832 r_chiral_restr 0.064 r_bond_refined_d 0.009 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 1219 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing