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Crystal structure of the Orange Carotenoid Protein 2 (OCP2) from Gloeocapsa sp. PCC 7428
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TUX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.2 M Magnesium formate dihydrate, 0.1 M Sodium acetate trihydrate pH 4.0, 18% w/v Polyethylene glycol monomethyl ether 5,000
Crystal Properties Matthews coefficient Solvent content 2.12 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.661 α = 90 b = 52.661 β = 90 c = 216.831 γ = 90
Symmetry Space Group P 43 21 2
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 2023-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.97920 SSRF BL17B1
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 1.8 72.28 98.2 0.134 0.153 0.072 0.996 6.6 4.3 29081
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 1.8 1.83 92.3 2.668 3.031 1.414 0.283 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 54.208 28909 1498 98.043 0.2 0.1974 0.1975 0.2481 0.2486 RANDOM 33.141
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] 0.668 0.668 -1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.282 r_dihedral_angle_3_deg 16.2 r_dihedral_angle_2_deg 13.96 r_dihedral_angle_1_deg 7.12 r_lrange_other 6.986 r_lrange_it 6.979 r_scangle_it 5.233 r_scangle_other 5.22 r_scbond_it 3.599 r_scbond_other 3.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.282 r_dihedral_angle_3_deg 16.2 r_dihedral_angle_2_deg 13.96 r_dihedral_angle_1_deg 7.12 r_lrange_other 6.986 r_lrange_it 6.979 r_scangle_it 5.233 r_scangle_other 5.22 r_scbond_it 3.599 r_scbond_other 3.561 r_mcangle_other 3.445 r_mcangle_it 3.442 r_mcbond_it 2.35 r_mcbond_other 2.347 r_angle_refined_deg 1.819 r_angle_other_deg 0.674 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.211 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.161 r_xyhbond_nbd_refined 0.136 r_nbd_other 0.117 r_symmetry_xyhbond_nbd_refined 0.112 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2340 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing