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Crystal structure of M. chilensis Mg662 protein complexed with GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AMS PDB 4AMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 Protein concentration: 5-12 mg/mL in 10 mM CAPS, 150 mM NaCl, pH 10.5
Reservoir solution: 0.05 M MES, 0.08 M Ammonium acetate pH 6.4
Soaking 0.5 mM GTP, UV treatment 5 minutes
Crystal Properties Matthews coefficient Solvent content 4.53 72.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.36 α = 90 b = 99.36 β = 90 c = 168.994 γ = 90
Symmetry Space Group P 43 21 2
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 2012-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1
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 2.26 168.99 100 0.127 0.037 0.993 13 13.1 40442 54.56
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 2.26 2.61 100 0.689 0.195 0.933 4 13.3 13906
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 FREE R-VALUE PDB 4AMS 2.26 38.88 1.35 40348 2017 99.99 0.1922 0.1908 0.1967 0.2171 0.2184 62.9484
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 12.752 f_angle_d 0.752 f_chiral_restr 0.028 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3054 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing XDS data reduction PDB_EXTRACT data extraction