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Mutant F105L of recombinant beta-lactoglobulin
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 8 293 2.4 M ammonium sulfate in 0.5 M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.79 α = 90 b = 52.79 β = 90 c = 108.82 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 PIXEL RIGAKU HyPix-3000 2020-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.5406
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 19.65 98.8 0.055 0.065 0.033 0.999 11 3.3 12244
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 2.05 99.3 0.637 0.797 0.472 0.465 1.7 2.6
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 19.65 12211 1088 98.23 0.204 0.20432 0.2002 0.2065 0.2464 0.2555 RANDOM 39.334
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] -0.011 -0.006 -0.011 0.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.017 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 7.962 r_lrange_it 6.709 r_lrange_other 6.686 r_dihedral_angle_4_deg 5.243 r_scangle_it 4.092 r_scangle_other 4.014 r_mcangle_it 3.773 r_mcangle_other 3.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.017 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 7.962 r_lrange_it 6.709 r_lrange_other 6.686 r_dihedral_angle_4_deg 5.243 r_scangle_it 4.092 r_scangle_other 4.014 r_mcangle_it 3.773 r_mcangle_other 3.772 r_scbond_it 2.556 r_scbond_other 2.508 r_mcbond_other 2.396 r_mcbond_it 2.395 r_angle_refined_deg 1.836 r_angle_other_deg 1.379 r_nbd_other 0.284 r_symmetry_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.198 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.163 r_nbtor_refined 0.161 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1174 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 17
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction