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Mutant L39K 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 3.0 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.56 α = 90 b = 53.56 β = 90 c = 110.88 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 2014-11-06 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 2.4 14.26 98.1 0.057 0.067 0.034 0.998 12.9 3.5 7446
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 2.4 2.49 97.6 0.653 0.83 0.502 0.714 1.4 2.5
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 2.401 13.753 7437 1075 97.279 0.204 0.20297 0.1938 0.2 0.2663 0.2714 RANDOM 50.562
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] -0.213 -0.106 -0.213 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_dihedral_angle_3_deg 18.301 r_dihedral_angle_4_deg 8.348 r_dihedral_angle_1_deg 7.94 r_lrange_it 5.954 r_lrange_other 5.95 r_scangle_it 4 r_scangle_other 3.997 r_mcangle_it 3.972 r_mcangle_other 3.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_dihedral_angle_3_deg 18.301 r_dihedral_angle_4_deg 8.348 r_dihedral_angle_1_deg 7.94 r_lrange_it 5.954 r_lrange_other 5.95 r_scangle_it 4 r_scangle_other 3.997 r_mcangle_it 3.972 r_mcangle_other 3.97 r_mcbond_it 2.46 r_mcbond_other 2.46 r_scbond_it 2.456 r_scbond_other 2.454 r_angle_refined_deg 1.779 r_angle_other_deg 1.233 r_nbd_other 0.243 r_symmetry_nbd_other 0.2 r_nbd_refined 0.198 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.138 r_symmetry_nbd_refined 0.137 r_symmetry_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1150 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 16
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction