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Human dynein light chain (DYNLL2) in complex with an in vitro evolved peptide (Ac-SRGTQTE).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CMI PDB ENTRY 1CMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 HANGING DROP VAPOR DIFFUSION AT 293K WITH A RESERVOIR SOLUTION 31% PEG 4000, 0.4 M NH4AC, 0.1 M NAAC PH 4.6, 2UL RESERVOIR SOLUTION AND 2UL PROTEIN SOLUTION
Crystal Properties Matthews coefficient Solvent content 1.7 27.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.6 α = 90 b = 64 β = 90 c = 151.84 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 CCD ADSC QUANTUM 315r 2009-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.31 151.84 96 0.07 15.66 7.6 81872 2 10.5
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 1.31 1.34 67.1 0.48 2.93 3.53
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 PDB ENTRY 1CMI 1.31 151.84 77776 4096 95.96 0.12447 0.12276 0.1336 0.15636 0.1635 RANDOM 10.471
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] 0.42 -0.06 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.095 r_dihedral_angle_4_deg 14.427 r_dihedral_angle_3_deg 12.936 r_scangle_it 7.464 r_dihedral_angle_1_deg 6.368 r_scbond_it 5.092 r_mcangle_it 3.49 r_mcbond_it 2.405 r_angle_refined_deg 2.01 r_rigid_bond_restr 1.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.095 r_dihedral_angle_4_deg 14.427 r_dihedral_angle_3_deg 12.936 r_scangle_it 7.464 r_dihedral_angle_1_deg 6.368 r_scbond_it 5.092 r_mcangle_it 3.49 r_mcbond_it 2.405 r_angle_refined_deg 2.01 r_rigid_bond_restr 1.382 r_angle_other_deg 1.065 r_mcbond_other 0.955 r_chiral_restr 0.135 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3040 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing