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Crystal structure of the carbonic anhydrase-like domain of CcmM in complex with the C-terminal 17 residues of CcaA from Synechococcus elongatus (strain PCC 7942)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% PEG-3350 and 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.365 α = 90 b = 89.365 β = 90 c = 129.835 γ = 120
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 2020-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99989 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.63 37.08 98.8 0.03 0.031 1 45.4 18.4 24740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.632 1.661 0.684 0.725 0.865
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 7O4Z 1.63 37.08 23554 1186 98.81 0.1785 0.1773 0.1886 0.1997 0.2053 RANDOM 34.751
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] -0.03 -0.02 -0.03 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.375 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_4_deg 13.585 r_dihedral_angle_1_deg 6.627 r_angle_refined_deg 2.099 r_angle_other_deg 1.495 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.015 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.375 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_4_deg 13.585 r_dihedral_angle_1_deg 6.627 r_angle_refined_deg 2.099 r_angle_other_deg 1.495 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1376 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing