☰ Navigation Tabs
Crystal structure of human mixed lineage kinase MAP3K10 SH3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OEB PDB entries 1OEB,1FMK experimental model PDB 1FMK PDB entries 1OEB,1FMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2M Sodium malonate, 0.1M Bis-tris-propane pH 8.5, 20.0% PEG 3350, 10.0% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.68 α = 90 b = 69.68 β = 90 c = 103.98 γ = 120
Symmetry Space Group P 32 1 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 MARMOSAIC 225 mm CCD 2007-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00234 SLS X10SA
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 2 52.19 100 0.066 0.066 21.1 8.4 19798 19798
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 2 2.11 100 0.739 0.739 4 8.2
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 PDB entries 1OEB,1FMK 2 52.19 18749 18749 1013 99.92 0.19093 0.19093 0.1889 0.1935 0.23014 0.232 RANDOM 40.878
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] 0.86 0.43 0.86 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.29 r_dihedral_angle_4_deg 21.537 r_dihedral_angle_3_deg 12.797 r_scangle_it 6.767 r_dihedral_angle_1_deg 6.075 r_scbond_it 5.108 r_mcangle_it 3.654 r_mcbond_it 2.855 r_angle_refined_deg 1.378 r_mcbond_other 0.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.29 r_dihedral_angle_4_deg 21.537 r_dihedral_angle_3_deg 12.797 r_scangle_it 6.767 r_dihedral_angle_1_deg 6.075 r_scbond_it 5.108 r_mcangle_it 3.654 r_mcbond_it 2.855 r_angle_refined_deg 1.378 r_mcbond_other 0.909 r_angle_other_deg 0.846 r_symmetry_vdw_other 0.272 r_nbd_other 0.204 r_nbtor_refined 0.19 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.139 r_nbtor_other 0.088 r_chiral_restr 0.079 r_symmetry_vdw_refined 0.079 r_symmetry_hbond_refined 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1758 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing