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Crystal structure of the rat endophilin-A1 SH3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GCQ PDB entry 1GCQ, chain A, Non-conserved residue pruned to CB atom using CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 20% methyl-2,4-pentanediol, 0.1M sodium acetate, 0.05M calcium chloride, 10mM 2-mercaptoethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.338 α = 90 b = 34.156 β = 107.79 c = 62.729 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 4 2007-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97720 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.4 30 96.3 0.031 30.2 3 24510 23667 2 8.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.5 85.5 0.071 11.1 1.9 4701
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1GCQ, chain A, Non-conserved residue pruned to CB atom using CHAINSAW 1.4 30 24901 23667 1234 96.56 0.12837 0.12702 0.15358 0.1757 RANDOM 13.739
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] 1 0.14 -0.27 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.769 r_dihedral_angle_4_deg 22.324 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 6.311 r_sphericity_free 6.116 r_scangle_it 3.908 r_sphericity_bonded 3.734 r_scbond_it 3.697 r_rigid_bond_restr 3.433 r_mcangle_it 2.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.769 r_dihedral_angle_4_deg 22.324 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 6.311 r_sphericity_free 6.116 r_scangle_it 3.908 r_sphericity_bonded 3.734 r_scbond_it 3.697 r_rigid_bond_restr 3.433 r_mcangle_it 2.004 r_mcbond_it 1.405 r_angle_refined_deg 1.402 r_nbtor_refined 0.322 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.193 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1174 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 2
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling