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Mutant L39Y 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 7.1 293 2.2 M ammonium sulfate in 0.5 M Tris-HCl pH 7.1
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.27 α = 90 b = 53.27 β = 90 c = 109.89 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 2015-03-15 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 13.74 99.4 0.058 0.07 0.038 0.998 7.7 2.7 11001
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 98.5 0.223 0.3 0.199 0.884 2 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 2.1 13.661 10981 1066 99.133 0.208 0.208 0.2008 0.2094 0.2754 0.2797 RANDOM 36.239
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] 0.075 0.037 0.075 -0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.049 r_dihedral_angle_3_deg 16.547 r_lrange_other 11.821 r_lrange_it 11.807 r_scangle_it 11.433 r_scangle_other 11.427 r_scbond_it 10.248 r_scbond_other 10.24 r_mcangle_it 8.631 r_mcangle_other 8.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.049 r_dihedral_angle_3_deg 16.547 r_lrange_other 11.821 r_lrange_it 11.807 r_scangle_it 11.433 r_scangle_other 11.427 r_scbond_it 10.248 r_scbond_other 10.24 r_mcangle_it 8.631 r_mcangle_other 8.625 r_dihedral_angle_4_deg 7.997 r_mcbond_it 7.607 r_mcbond_other 7.603 r_dihedral_angle_1_deg 7.219 r_angle_refined_deg 1.686 r_angle_other_deg 1.239 r_nbd_other 0.294 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.157 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1161 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 15
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction