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Crystal structure of a DM9 domain containing protein from Crassostrea gigas with K43A mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DM9CP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1M Bis-Tris pH 6.0
25%PEG 3350
0.2M Lithium sulphate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.88 57.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.93 α = 101.34 b = 97.96 β = 107.87 c = 101.42 γ = 106.46
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 2016-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.000 SRS PX10.1
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 1.6 20 95.5 0.052 16.3 3.5 273332 261115
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 1.6 1.65 89 1.07 3.5 24071
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT DM9CP 1.6 19.987 1.94 261071 13054 95.68 0.1702 0.1689 0.1693 0.1964 0.1965
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.386 f_angle_d 0.793 f_chiral_restr 0.062 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13092 Nucleic Acid Atoms Solvent Atoms 2031 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing