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Crystal structure of the carbonic anhydrase-like domain of CcmM from Synechococcus elongatus (strain PCC 7942)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KWC
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 = 89.741 α = 90 b = 89.741 β = 90 c = 130.79 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 PILATUS3 2M 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.667 66.812 99.9 0.081 0.028 0.998 13.8 9.7 23881
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 1.667 1.696 100 0.96 0.319 0.823 2.3 10
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 3KWC 1.67 66.81 22708 1173 99.95 0.1656 0.1637 0.1781 0.1998 0.2117 RANDOM 28.717
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.993 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_4_deg 12.87 r_dihedral_angle_1_deg 6.564 r_angle_refined_deg 1.948 r_angle_other_deg 1.433 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.993 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_4_deg 12.87 r_dihedral_angle_1_deg 6.564 r_angle_refined_deg 1.948 r_angle_other_deg 1.433 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1248 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing