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Crystal structure of a shortened IpgC variant with two bound Magnesium and two bound Chlorine atoms each
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30% PEG 4000, 0.05 M TRIS (pH 7.0),
0.3 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.34 47.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.554 α = 90 b = 57.554 β = 90 c = 159.979 γ = 120
Symmetry Space Group P 32 2 1
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 6M 2019-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.58 50 99.6 0.055 0.999 16.64 4.89 43023 18.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.66 99.4 0.57 0.906 2.42 4.72
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3gyz 1.58 47.59 1.36 42965 2138 99.52 0.1773 0.1753 0.1763 0.2152 0.2158 Random selection 25.67
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 16.2168 f_angle_d 0.9509 f_chiral_restr 0.0537 f_bond_d 0.0081 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2160 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing PHENIX refinement Coot model building