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Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) complexed with zeaxanthin
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 0.7 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.688 α = 90 b = 66.528 β = 90 c = 120.516 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 2022-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 60.26 98 0.125 0.133 0.043 0.834 15 10.6 17115 35.86
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 95.5 1.169 1.229 0.371 0.657 10.3
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 2 60.26 16785 792 96 0.2375 0.2351 0.2461 0.2839 0.3056 RANDOM 41.54
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] 6.4326 5.5717 -12.0042
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.29 t_omega_torsion 3.55 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.29 t_omega_torsion 3.55 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1856 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 20
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing BUSTER refinement PDB_EXTRACT data extraction