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Lipocalin-like Milk protein-2 - E38A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BKX 7BKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0 (0.002 M Zinc sulfate heptahydrate; 0.08 M HEPES pH 7.0; 25 % v/v Jeffamine
Crystal Properties Matthews coefficient Solvent content 3.95 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.771 α = 90 b = 52.337 β = 90 c = 136.348 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M double crystal 2022-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.07 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.95 38.18 99.9 0.129 0.054 0.998 11.5 6.6 6461 76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.13 100 2 0.83 0.58 1 6.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7BKX 2.951 38.18 6430 323 99.798 0.237 0.2345 0.2356 0.2936 0.272 98.323
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] 6.649 0.7 -7.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.414 r_lrange_other 17.345 r_lrange_it 17.344 r_dihedral_angle_2_deg 16.293 r_dihedral_angle_6_deg 13.73 r_mcangle_it 12.306 r_mcangle_other 12.298 r_scangle_it 11.967 r_scangle_other 11.962 r_mcbond_it 7.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.414 r_lrange_other 17.345 r_lrange_it 17.344 r_dihedral_angle_2_deg 16.293 r_dihedral_angle_6_deg 13.73 r_mcangle_it 12.306 r_mcangle_other 12.298 r_scangle_it 11.967 r_scangle_other 11.962 r_mcbond_it 7.836 r_mcbond_other 7.835 r_scbond_it 7.747 r_scbond_other 7.742 r_dihedral_angle_1_deg 7.458 r_angle_refined_deg 1.361 r_angle_other_deg 0.432 r_nbd_refined 0.215 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.173 r_symmetry_nbd_refined 0.122 r_nbd_other 0.093 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.054 r_symmetry_metal_ion_refined 0.033 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1235 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing