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Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform, S206V 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 BISTRIS propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.985 α = 90 b = 65.333 β = 90 c = 118.978 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 2022-03-25 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 2.5 21.03 99.8 0.162 0.173 0.06 0.994 8.6 8.2 8648 51.05
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 2.5 2.6 99.9 0.908 0.964 0.322 0.842 8.8
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 2.5 21.03 8610 393 99.7 0.2007 0.1981 0.2091 0.2536 0.2738 RANDOM 40.75
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] 3.0563 4.7668 -7.8231
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.54 t_omega_torsion 3.28 t_angle_deg 1.02 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 17.54 t_omega_torsion 3.28 t_angle_deg 1.02 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 1788 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing BUSTER refinement PDB_EXTRACT data extraction