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Homo-dimer crystal structure of geranylgeranyl diphosphate synthases 1 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 7 293.15 2.0 M sodium malonate, 20% PEG 3350, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.022 α = 90 b = 74.118 β = 90.81 c = 71.288 γ = 90
Symmetry Space Group P 1 21 1
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 2 38.1 99.2 19 4 39062
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 2.002 38.056 1.34 39051 1960 99.17 0.1884 0.187 0.1915 0.2135 0.214 33.0425
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 13.787 f_angle_d 1.374 f_chiral_restr 0.066 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4322 Nucleic Acid Atoms Solvent Atoms 226 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 data reduction