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Crystal structure of the c-src-SH3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HDA PDB ENTRY 2HDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 288 1.7M Ammonium sulphate, 5% PEG300, 10% glycerol, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.07 59.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.596 α = 90 b = 46.596 β = 90 c = 128.064 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 110 CCD Mar CCD-165 2008-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.97 ESRF BM16
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 40.357 95.6 0.078 0.078 4.701 7.1 19644 22.104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 95 0.543 0.543 1.4 7.1 2838
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2HDA 1.65 20 17923 917 94.96 0.206 0.206 0.2662 0.222 0.2654 RANDOM 19.079
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] 0.71 0.36 0.71 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.031 r_dihedral_angle_3_deg 11.248 r_dihedral_angle_4_deg 8.283 r_dihedral_angle_1_deg 5.039 r_scangle_it 2.631 r_mcangle_it 2.59 r_angle_refined_deg 2.029 r_mcbond_it 1.945 r_scbond_it 1.805 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.031 r_dihedral_angle_3_deg 11.248 r_dihedral_angle_4_deg 8.283 r_dihedral_angle_1_deg 5.039 r_scangle_it 2.631 r_mcangle_it 2.59 r_angle_refined_deg 2.029 r_mcbond_it 1.945 r_scbond_it 1.805 r_nbtor_refined 0.304 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.114 r_symmetry_hbond_refined 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 922 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 59
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection