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Structure of an ADP ribosylation factor from Entamoeba histolytica HM-1:IMSS bound to Mg-GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R8S PDB ENTRY 1R8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 15% ethanol, 0.1M Tris, Cryoprotection 25% Ethylene glycol, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.54 α = 90 b = 40.66 β = 97.45 c = 78.95 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2010-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 19.729 93.4 0.06 0.069 15.97 34091 -3 15.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 96.9 0.431 0.486 3.24
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1R8S 1.8 19.729 1.34 34061 1702 93.44 0.2252 0.2226 0.2243 0.272 0.2739 RANDOM 25.5495
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 14.374 f_angle_d 1.127 f_chiral_restr 0.052 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2492 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data scaling XSCALE data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction REFMAC refinement