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Mutant F105A of recombinant beta-lactoglobulin in complex with endogenous ligand
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 8.5 293 2.6 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.34 α = 90 b = 53.34 β = 90 c = 112.31 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 100 CCD AGILENT ATLAS CCD 2015-12-09 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 1.9 15.4 99.7 0.067 0.081 0.045 0.997 12 2.7 15168
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 1.9 1.95 99.8 0.492 0.651 0.419 0.677 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 (All) 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 1.9 13.789 15127 1036 99.552 0.189 0.1891 0.1854 0.1953 0.2432 0.252 RANDOM 27.742
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] 0.004 0.002 0.004 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 7.472 r_lrange_it 5.441 r_lrange_other 5.436 r_scangle_it 3.12 r_scangle_other 3.06 r_mcangle_it 2.482 r_mcangle_other 2.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 7.472 r_lrange_it 5.441 r_lrange_other 5.436 r_scangle_it 3.12 r_scangle_other 3.06 r_mcangle_it 2.482 r_mcangle_other 2.482 r_scbond_it 1.95 r_scbond_other 1.905 r_angle_refined_deg 1.638 r_mcbond_it 1.54 r_mcbond_other 1.54 r_angle_other_deg 1.349 r_nbd_refined 0.196 r_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.154 r_symmetry_nbd_refined 0.093 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.012 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 19
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction