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Crystal structure of the cargo-binding domain from the plant class XI myosin (MyoXIk)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 75 mM Bis-Tris pH 7.5, 0.2 M MgCl2, 25% (w/v) PEG 3350 and 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.062 α = 90 b = 54.333 β = 96.6 c = 113.432 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 S 6M 2016-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.35 47.36 99.29 0.1264 0.996 7.08 3.2 37294 53.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.434 1.368 0.456
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 4J5L 2.35 47.36 35418 1875 99.32 0.2343 0.2323 0.2355 0.2729 0.2753 RANDOM 66.004
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] -2.22 0.8 4.96 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.944 r_dihedral_angle_3_deg 15.841 r_dihedral_angle_4_deg 13.171 r_dihedral_angle_1_deg 4.706 r_angle_refined_deg 1.145 r_angle_other_deg 1.064 r_chiral_restr 0.039 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.944 r_dihedral_angle_3_deg 15.841 r_dihedral_angle_4_deg 13.171 r_dihedral_angle_1_deg 4.706 r_angle_refined_deg 1.145 r_angle_other_deg 1.064 r_chiral_restr 0.039 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5557 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Arcimboldo phasing