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Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.1 M BIS-TRIS pH 6.5, 16% (w/v) PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.57 52.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.218 α = 90 b = 69.432 β = 90 c = 110.337 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 PIXEL DECTRIS PILATUS3 6M 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.98655 SSRF BL19U1
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 1.93 57.4 99.8 0.131 13.5 12.3 39526 31.25
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 1.93 1.96 0.899
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4LHW 1.93 43.19 1.36 37399 1816 94.55 0.1763 0.1743 0.1774 0.2182 0.2215 31.25
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.2635 f_angle_d 1.052 f_chiral_restr 0.0565 f_bond_d 0.0087 f_plane_restr 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3406 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 114
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction autoPROC data scaling PHENIX phasing