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Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform, W232F mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.5 M Sodium citrate tribasic dihydrate, 0.1 M BIS- TRIS propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.19 43.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.033 α = 90 b = 66.772 β = 90 c = 120.502 γ = 90
Symmetry Space Group C 2 2 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 PIXEL RIGAKU HyPix-6000HE 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
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 1.75 60.25 98.5 0.086 0.09 0.027 0.979 20.8 11.5 25252
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 1.75 1.78 84.8 0.848 0.952 0.418 0.609 4.8
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 7ZTQ 1.75 60.25 24006 1209 98.42 0.1836 0.1811 0.1919 0.2323 0.2346 RANDOM 22.825
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] 0.42 -0.67 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.511 r_dihedral_angle_3_deg 15.334 r_dihedral_angle_1_deg 7.54 r_angle_refined_deg 2.092 r_angle_other_deg 0.873 r_chiral_restr 0.137 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1817 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction