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Insights into dynein assembly from a dynein intermediate chain-light chain roadblock structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277.15 1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 3.54 65.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.18 α = 90 b = 107.18 β = 90 c = 65.41 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 133.15 CCD ADSC QUANTUM 315 2009-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 3 92.82 100 0.09 0.07 7.1 5.7 16845 2
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 3 3.15 100 0.442 0.402 1.9 5.7
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 2HZ5 3 92.8 16845 923 100 0.228 0.227 0.2257 0.249 0.2399 RANDOM 44.2
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.06 r_dihedral_angle_4_deg 25.082 r_dihedral_angle_3_deg 23.542 r_scangle_it 11.701 r_dihedral_angle_1_deg 7.222 r_scbond_it 6.822 r_mcangle_it 5.074 r_mcbond_it 2.486 r_angle_refined_deg 1.909 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.06 r_dihedral_angle_4_deg 25.082 r_dihedral_angle_3_deg 23.542 r_scangle_it 11.701 r_dihedral_angle_1_deg 7.222 r_scbond_it 6.822 r_mcangle_it 5.074 r_mcbond_it 2.486 r_angle_refined_deg 1.909 r_chiral_restr 0.132 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4180 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction iMOSFLM data reduction