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Crystal structure of the ILK/alpha-parvin core complex (MnATP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KMW PDB ENTRY 3KMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 277 50 mM Bis-Tris Propane, 12.5 (w/v) PEG 5000 MME, 5% (v/v) 1-propyl alcohol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.022 α = 90 b = 116.28 β = 101.53 c = 47.284 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944+ 2011-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.8 43.13 94.2 0.034 5.15 40605
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) 1.8 1.86 76.2 0.136 4.22
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3KMW 1.8 34.64 37526 1984 0.20583 0.20417 0.2039 0.23783 0.2315 RANDOM 26.042
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] 0.14 0.02 0.19 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.388 r_dihedral_angle_4_deg 16.791 r_dihedral_angle_3_deg 13.868 r_dihedral_angle_1_deg 5.719 r_scangle_it 3.285 r_scbond_it 2.326 r_mcangle_it 1.537 r_angle_refined_deg 1.472 r_mcbond_it 0.972 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.388 r_dihedral_angle_4_deg 16.791 r_dihedral_angle_3_deg 13.868 r_dihedral_angle_1_deg 5.719 r_scangle_it 3.285 r_scbond_it 2.326 r_mcangle_it 1.537 r_angle_refined_deg 1.472 r_mcbond_it 0.972 r_nbtor_refined 0.304 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3157 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement CNS refinement StructureStudio data collection d*TREK data reduction d*TREK data scaling CNS phasing