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Crystal structure of Myosin V motor with essential light chain-nucleotide-free
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MYS PDB ENTRY 2MYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 6% PEG8000 (W/V), 50MM MOPS PH 6.5, 2MM DTT, 2MM NAN3
Crystal Properties Matthews coefficient Solvent content 2.8 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.933 α = 90 b = 98.247 β = 101.43 c = 111.378 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 2002-11-15 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 2.05 40 96.8 0.06 14 2.9 69115 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 2.05 2.12 88.4 0.335 2.34 2
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 2MYS 2.05 40 65624 3474 96.8 0.222 0.22 0.2233 0.264 0.2629 RANDOM 39.16
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] 1.12 0.22 -0.91 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.388 r_scangle_it 3.416 r_scbond_it 2.067 r_mcangle_it 1.509 r_angle_refined_deg 1.3 r_mcbond_it 0.823 r_angle_other_deg 0.791 r_symmetry_vdw_other 0.256 r_nbd_other 0.237 r_nbd_refined 0.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.388 r_scangle_it 3.416 r_scbond_it 2.067 r_mcangle_it 1.509 r_angle_refined_deg 1.3 r_mcbond_it 0.823 r_angle_other_deg 0.791 r_symmetry_vdw_other 0.256 r_nbd_other 0.237 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.135 r_nbtor_other 0.085 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6919 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing