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Microtubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SRY pdb entry 1SRY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 Protein was changed into crystallization buffer (20mM K-HEPES, pH7.5, 10% w/v glycerol, 0.2mM PMSF, 1mM DTT, 4mM Mg-ATP, 0.01% Na-Azide) and concentrated to 18 mg/ml. Crystallization was carried out by setting hanging drops containing 2 ul of protein, (diluted to 13.5mg/ml with 20mM K-Hepes, pH 7.5, 10% glycerol), 0.3 ul 70% glycerol and 1.8 ul of precipitant (20% PEG 4000, 200mM Ammonium sulfate, 100mM Bis-Tris, pH 5.5) over 500ml of the same precipitant solution. Crystals appeared within one day and were of dimensions up to 200 um., VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.302 α = 90 b = 144.302 β = 90 c = 159.946 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 77 CCD ADSC QUANTUM 315 2008-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.5 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.27 49.27 99.4 18.6 5.6 57296 57296 2 2
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) 2.27 2.35 94.5 62 2
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 (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 entry 1SRY 2.27 49.27 2 54226 54226 2867 99.08 0.19954 0.19702 0.2219 0.24655 0.2581 RANDOM 55.202
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] -0.06 -0.03 -0.06 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.274 r_dihedral_angle_3_deg 20.453 r_dihedral_angle_4_deg 19.884 r_dihedral_angle_1_deg 6.618 r_scangle_it 4.409 r_scbond_it 2.767 r_angle_refined_deg 1.923 r_mcangle_it 1.515 r_mcbond_it 0.845 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.274 r_dihedral_angle_3_deg 20.453 r_dihedral_angle_4_deg 19.884 r_dihedral_angle_1_deg 6.618 r_scangle_it 4.409 r_scbond_it 2.767 r_angle_refined_deg 1.923 r_mcangle_it 1.515 r_mcbond_it 0.845 r_chiral_restr 0.135 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8420 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling