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Crystal structure of EhRho1 bound to GDP and Magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPF PDB ENTRY 1DPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 EhRho1 at 15 mg/mL in crystallization buffer (50 mM Tris pH 8.0, 250 mM NaCl, 2.5% (v/v) glycerol, 5 mM DTT, 50 microM GDP, 1 mM magnesium chloride) was mixed 1:1 with and equilibrated against crystallization solution (1.5 M ammonium sulfate, 100 mM Tris pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.11 41.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.3 α = 90 b = 54.476 β = 90 c = 132.285 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate custom 2010-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 28.324 99.4 0.047 21.9 2.5 27432 27267
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 99.4 0.187 2.5 1.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1DPF 1.95 28.324 0.12 27432 27158 1366 99.58 0.1586 0.1565 0.1555 0.1974 0.198
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] -0.0786 0.1266 -0.048
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16 f_angle_d 1.26 f_chiral_restr 0.088 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2759 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 73
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling