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Human dynein light chain (DYNLL2) in complex with an in vitro evolved peptide dimerized by leucine zipper
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XQQ PDB ENTRY 2XQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 20% PEG8000, 0.2 M MgCl2, 0.1 M TRIS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.839 α = 90 b = 68.415 β = 90 c = 101.677 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC BLUE 2010-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 2.9 56.76 94.4 0.131 6.4 3.23 8273 -3
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 2.9 3 96.6 0.576 1.5 3.12
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XQQ 2.9 42.31 7886 7886 385 94.4 0.25 0.248 0.2436 0.295 0.2877 RANDOM 52.8
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] -3.09 1.47 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 23.12 r_dihedral_angle_3_deg 19.644 r_dihedral_angle_1_deg 5.772 r_angle_other_deg 2.416 r_angle_refined_deg 1.119 r_scangle_it 0.837 r_scbond_it 0.523 r_mcangle_it 0.305 r_mcbond_it 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 23.12 r_dihedral_angle_3_deg 19.644 r_dihedral_angle_1_deg 5.772 r_angle_other_deg 2.416 r_angle_refined_deg 1.119 r_scangle_it 0.837 r_scbond_it 0.523 r_mcangle_it 0.305 r_mcbond_it 0.175 r_chiral_restr 0.063 r_mcbond_other 0.053 r_bond_refined_d 0.011 r_bond_other_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1975 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling