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Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform, D162L 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 0.7 M Sodium citrate tribasic dihydrate, 0.1 M BIS- TRIS propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.175 α = 90 b = 67.115 β = 90 c = 121.123 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 DECTRIS EIGER X 16M 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.98 ESRF MASSIF-3
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 1.9 46 97.3 0.179 0.203 0.092 0.967 8.6 4.5 19947
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 1.9 1.94 97.2 1.573 1.776 0.799 0.743 4.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7ZTQ 1.9 46 18879 1058 96.39 0.2084 0.2059 0.2514 0.3004 RANDOM 33.411
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] 3.37 -1.4 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.776 r_dihedral_angle_2_deg 15.345 r_dihedral_angle_1_deg 8.36 r_angle_refined_deg 2.158 r_angle_other_deg 0.947 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.008 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1803 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction