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Apo structure of the Grb7 SH2 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.1 M sodium malonate, 0.1 M HEPES pH 7.0, 0.5%(v/v) Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.85 56.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84 α = 90 b = 84 β = 90 c = 75.95 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 CCD ADSC QUANTUM 315r 2010-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 27.495 100 0.106 0.111 0.033 16.7 11.3 28306 28306 16.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.549 0.549 0.171 1.4 11.3 4125
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 FREE R-VALUE 2QMS 1.8 27.495 1.36 28281 1424 99.98 0.1705 0.1691 0.1717 0.1982 0.2001 21.6853
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 12.028 f_angle_d 1.192 f_chiral_restr 0.049 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1819 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing