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Engineered beta-lactoglobulin: variant L39Y in complex with endogenous ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HTD
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 7.1
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.307 α = 90 b = 53.307 β = 90 c = 110.424 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 2015-03-25 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 2.5 14.75 99.4 0.062 0.074 0.039 0.997 9 3.2 6635
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 2.5 2.61 100 0.393 0.484 0.277 0.845 2.8
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 5HTD 2.5 14.75 5971 662 99.09 0.2013 0.1946 0.2024 0.2624 0.2602 RANDOM 45.585
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] -0.03 -0.01 -0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.676 r_dihedral_angle_4_deg 20.812 r_dihedral_angle_3_deg 16.499 r_dihedral_angle_1_deg 7.233 r_angle_refined_deg 1.505 r_angle_other_deg 1.171 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.676 r_dihedral_angle_4_deg 20.812 r_dihedral_angle_3_deg 16.499 r_dihedral_angle_1_deg 7.233 r_angle_refined_deg 1.505 r_angle_other_deg 1.171 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1171 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 30
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing