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Structure of the GcpE-HMBPP complex from Thermus thermophilius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G9P GcpE-MEcPP, PDB entry 4g9p
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 0.6 L enzyme solution, containing 5 mM HMBPP, and 0.6 L precipitant composed of 45% pentaerythritol propoxylate 426, 0.1 M MES pH 6.0, 0.4 M KCl, 0.1% NaN3 (JBScreen Pentaerythritol 1, C6, Jena Bioscience) and 0.1 L; random microseeding, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.25 α = 90 b = 63.25 β = 90 c = 372.12 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 PSI PILATUS 6M 2013-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.972 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.65 62 94.4 0.09 0.089 16.7 7.3 95074 95074
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 73.6 2.3 2.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT GcpE-MEcPP, PDB entry 4g9p 1.65 19.946 1.37 94961 94899 4903 94.43 0.128 0.1202 0.1701 0.1562
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 14.421 f_angle_d 1.324 f_chiral_restr 0.048 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6200 Nucleic Acid Atoms Solvent Atoms 2216 Heterogen Atoms 70
Software Software Software Name Purpose XDS data scaling PHASER phasing PHENIX refinement XDS data reduction