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Ultra-high resolution crystal structure of caprine Beta-lactoglobulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 10% (w/v) PEG 20000, 20% (v/v) PEG MME 550 and 100 mM MES/imidazole
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.32 α = 90 b = 54.58 β = 107.31 c = 56.39 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2014-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.17 53.836 99.6 0.081 0.087 0.032 12.2 7.2 101724 101724
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.23 99.1 0.694 0.694 0.276 2.6 7.1 14688
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 1bso 1.17 23.14 101707 2042 99.59 0.1322 0.1316 0.1312 0.1591 0.1584 RANDOM 15.438
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 -0.04 -0.12 0.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.944 r_dihedral_angle_2_deg 32.275 r_dihedral_angle_3_deg 12.954 r_dihedral_angle_4_deg 10.93 r_sphericity_bonded 10.557 r_dihedral_angle_1_deg 6.472 r_mcangle_it 1.923 r_angle_other_deg 1.878 r_angle_refined_deg 1.655 r_rigid_bond_restr 1.569
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.944 r_dihedral_angle_2_deg 32.275 r_dihedral_angle_3_deg 12.954 r_dihedral_angle_4_deg 10.93 r_sphericity_bonded 10.557 r_dihedral_angle_1_deg 6.472 r_mcangle_it 1.923 r_angle_other_deg 1.878 r_angle_refined_deg 1.655 r_rigid_bond_restr 1.569 r_mcbond_it 1.417 r_mcbond_other 1.412 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2521 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 6
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building