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Crystal structure of the yeast Bzz1 first SH3 domain at 0.97-A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.74 α = 90 b = 36.74 β = 90 c = 76.55 γ = 90
Symmetry Space Group P 43 21 2
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 MARRESEARCH 2005-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.976 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.97 20 100 0.086 17.4 10.2 31881 31881 -3 -3 8.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 0.97 1 100 0.575 3.7 7.3 2730
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 (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 1E6H 0.97 20 -3 31881 31881 1619 100 0.12407 0.12407 0.12309 0.1356 0.1422 0.1587 RANDOM 6.294
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] 0.22 0.22 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.456 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_4_deg 11.19 r_sphericity_free 10.099 r_dihedral_angle_1_deg 7.018 r_scangle_it 4.185 r_scbond_it 3.435 r_sphericity_bonded 3.307 r_mcangle_it 2.473 r_mcbond_it 2.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.456 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_4_deg 11.19 r_sphericity_free 10.099 r_dihedral_angle_1_deg 7.018 r_scangle_it 4.185 r_scbond_it 3.435 r_sphericity_bonded 3.307 r_mcangle_it 2.473 r_mcbond_it 2.087 r_angle_refined_deg 1.904 r_rigid_bond_restr 1.685 r_mcbond_other 0.951 r_angle_other_deg 0.86 r_symmetry_vdw_other 0.263 r_symmetry_hbond_refined 0.262 r_xyhbond_nbd_refined 0.25 r_nbd_refined 0.211 r_nbd_other 0.186 r_symmetry_vdw_refined 0.171 r_nbtor_refined 0.165 r_chiral_restr 0.117 r_nbtor_other 0.092 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 535 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing