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Crystal structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria, Yb-derivative at 2.8 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 292 300 MM NA ACETATE, 20% PEG2000 MME,
REMARK 280 100 MM HEPES BUFFER, PH 8.0; before data collection crystals were soaked for 30 min in a solution containing 25% PEG2000MME, 0.2 M sodium acetate, 0.1 M HEPES, pH 8.0 and 0.1 M Yb-HPDO3A
Crystal Properties Matthews coefficient Solvent content 2.13 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.89 α = 90 b = 120.734 β = 90 c = 117.548 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 PILATUS3 S 6M mirrors 2015-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.385 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.79 66 97.8 0.095 14.5 6.5 13464 51.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.87 61.2 0.63 1.77 2.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.79 10 13151 677 95.52 0.18764 0.18593 0.1952 0.21948 0.2181 RANDOM 53.449
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] 5.23 2.17 -7.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.83 r_dihedral_angle_3_deg 17.404 r_dihedral_angle_4_deg 17.364 r_long_range_B_refined 6.247 r_long_range_B_other 6.245 r_dihedral_angle_1_deg 5.595 r_scangle_other 3.868 r_mcangle_it 3.662 r_mcangle_other 3.661 r_scbond_it 2.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.83 r_dihedral_angle_3_deg 17.404 r_dihedral_angle_4_deg 17.364 r_long_range_B_refined 6.247 r_long_range_B_other 6.245 r_dihedral_angle_1_deg 5.595 r_scangle_other 3.868 r_mcangle_it 3.662 r_mcangle_other 3.661 r_scbond_it 2.258 r_scbond_other 2.257 r_mcbond_it 2.139 r_mcbond_other 2.139 r_angle_refined_deg 1.779 r_angle_other_deg 1.027 r_chiral_restr 0.122 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling CRANK2 phasing