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Crystal structure of the SH3 domain from IRSp53 (BAIAP2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BG5 1BG5, 1Y6E, 1GNE, 1DUG and 3QMZ experimental model PDB 1Y6E 1BG5, 1Y6E, 1GNE, 1DUG and 3QMZ experimental model PDB 1GNE 1BG5, 1Y6E, 1GNE, 1DUG and 3QMZ experimental model PDB 1DUG 1BG5, 1Y6E, 1GNE, 1DUG and 3QMZ experimental model PDB 3QMZ 1BG5, 1Y6E, 1GNE, 1DUG and 3QMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2M ammonium acetate, 0.1M Tris-HCl pH 8.5, 30% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.96 α = 90 b = 36.64 β = 90 c = 58.11 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 CCD ADSC QUANTUM 315 2010-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.5 31 99.8 9.7 4.6 10736 10716 -3 -3 17.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.52 100 2.43 4.5 408
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1BG5, 1Y6E, 1GNE, 1DUG and 3QMZ 1.5 23.2 10716 10700 536 99.7 0.198 0.198 0.197 0.1982 0.219 0.2279 Random
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] -4.1656 -7.8872 12.0528
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.548 f_angle_d 0.944 f_chiral_restr 0.054 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 530 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 36
Software Software Software Name Purpose ADSC data collection PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling