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Oxidized, active structure of the beta-carboxysomal gamma-Carbonic Anhydrase, CcmM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KWD PDB entry 3KWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 58 mg/ml protein, 20% isopropanol, 30% PEG 4000, 0.1 M Na Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.9 α = 90 b = 105.04 β = 90 c = 196.13 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MAR scanner 345 mm plate Osmic multi-layer optics 2009-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 17 99.2 0.085 16.6 7.45 89407 89407 -3 -3 28.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.2 98.3 0.454 4.6 6.65 22120
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 3KWD 2 16.88 -3 -3 84679 84679 4569 99.36 0.20217 0.20217 0.19978 0.2042 0.24702 0.2529 RANDOM 20.409
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] 1.33 0.31 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.129 r_dihedral_angle_3_deg 13.165 r_dihedral_angle_4_deg 11.503 r_dihedral_angle_1_deg 6.297 r_scangle_it 1.497 r_angle_refined_deg 1.3 r_scbond_it 1.049 r_angle_other_deg 0.948 r_mcangle_it 0.546 r_mcbond_it 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.129 r_dihedral_angle_3_deg 13.165 r_dihedral_angle_4_deg 11.503 r_dihedral_angle_1_deg 6.297 r_scangle_it 1.497 r_angle_refined_deg 1.3 r_scbond_it 1.049 r_angle_other_deg 0.948 r_mcangle_it 0.546 r_mcbond_it 0.421 r_nbd_other 0.188 r_symmetry_vdw_other 0.187 r_nbd_refined 0.179 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.135 r_symmetry_vdw_refined 0.129 r_mcbond_other 0.111 r_chiral_restr 0.078 r_nbtor_other 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9356 Nucleic Acid Atoms Solvent Atoms 807 Heterogen Atoms 36
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XPREP data reduction