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Crystal structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria at 2.5 A resolution in P6322 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Protein at 6.08 mg/ml in 50 mM Bicine/KOH pH 7.8, 40 mM KCl, 0.132 mM AMP solution was mixed with reservoir solution containing 0.15 M KSCN, 0.1 M HEPES pH 7.0 and 18% PEG3350 containing 0.1 mM Guanidine hydrochloride. Cryoprotector - reservoir solution with 25% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 3.03 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.235 α = 90 b = 98.235 β = 90 c = 100.619 γ = 120
Symmetry Space Group P 63 2 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 PILATUS 6M 2016-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9184 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 100.62 99.9 0.084 0.027 0.999 23.4 18.5 10477 59.721
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.2 1.354 0.462 0.881 2.6 17.6
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 5NMU 2.5 85.07 9924 495 99.94 0.20038 0.19866 0.2028 0.23446 0.2434 RANDOM 74.6
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] 1.1 0.55 1.1 -3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.892 r_dihedral_angle_4_deg 24.723 r_dihedral_angle_3_deg 15.748 r_long_range_B_other 7.702 r_long_range_B_refined 7.694 r_dihedral_angle_1_deg 5.987 r_scangle_other 5.643 r_mcangle_other 4.203 r_mcangle_it 4.2 r_scbond_it 3.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.892 r_dihedral_angle_4_deg 24.723 r_dihedral_angle_3_deg 15.748 r_long_range_B_other 7.702 r_long_range_B_refined 7.694 r_dihedral_angle_1_deg 5.987 r_scangle_other 5.643 r_mcangle_other 4.203 r_mcangle_it 4.2 r_scbond_it 3.442 r_scbond_other 3.44 r_mcbond_it 2.621 r_mcbond_other 2.62 r_angle_refined_deg 1.732 r_angle_other_deg 1.012 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1351 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing