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Heterodimer crystal structure of geranylgeranyl diphosphate synthases 1 with GGPPS Recruiting Protein(OsGRP) from Oryza sativa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 16% PEG 10000, 0.1 M Bis-Tris, pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.35 71.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.062 α = 109.39 b = 102.981 β = 109.59 c = 103.486 γ = 109.13
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL CS-PAD CXI-1 2013-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.9798 SSRF BL17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.59 37.8 96.9 8.26 1.9 36920
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 5E8H 3.598 37.755 1.96 36881 1845 96.79 0.2525 0.2519 0.2714 0.2633 0.2803 90.3147
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 16.281 f_angle_d 2.542 f_chiral_restr 0.13 f_bond_d 0.013 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12244 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing HKL-2000 data reduction HKL-2000 data reduction HKL-2000 data reduction HKL-2000 data reduction HKL data reduction