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The structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.8 293 Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.888 α = 90 b = 114.121 β = 90 c = 140.506 γ = 90
Symmetry Space Group C 1 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 173 PIXEL DECTRIS PILATUS 300K 2018-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 .987 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 60 94 0.205 0.19 0.209 0.031 0.999 10.7 45.2 49538 93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.7 45.3 1.62 1.62 1.66 0.24 0.976 3.4 46.7
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 1BEB 2.3 57.06 43606 2327 99.46 0.20974 0.20681 0.2068 0.26097 0.2609 RANDOM 92.982
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] 110.93 -1.74 18.76 -129.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.383 r_long_range_B_refined 15.927 r_long_range_B_other 15.926 r_dihedral_angle_4_deg 15.919 r_dihedral_angle_3_deg 15.061 r_mcangle_it 11.171 r_mcangle_other 11.17 r_scangle_other 9.357 r_mcbond_other 8.173 r_mcbond_it 8.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.383 r_long_range_B_refined 15.927 r_long_range_B_other 15.926 r_dihedral_angle_4_deg 15.919 r_dihedral_angle_3_deg 15.061 r_mcangle_it 11.171 r_mcangle_other 11.17 r_scangle_other 9.357 r_mcbond_other 8.173 r_mcbond_it 8.172 r_dihedral_angle_1_deg 7.779 r_scbond_it 6.792 r_scbond_other 6.791 r_angle_refined_deg 1.109 r_angle_other_deg 1.022 r_chiral_restr 0.028 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.001 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7519 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing