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Crystal structure of Ragulator complex (p18 76-145)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 0.1 M Bis-Tris (pH 5.5), and 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.659 α = 90 b = 117.854 β = 90 c = 157.805 γ = 90
Symmetry Space Group C 2 2 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 RAYONIX MX225HE 2015-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.65 50.01 98.1 0.046 0.052 0.023 12.6 4.6 29802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 98.6 0.509 0.576 0.262 0.801 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.65 50.01 25354 1365 88.07 0.21799 0.21551 0.2156 0.2626 0.2626 RANDOM 60.279
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] 1.08 -4.26 3.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 52.543 r_dihedral_angle_2_deg 39.644 r_dihedral_angle_3_deg 19.255 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_1_deg 5.683 r_long_range_B_refined 4.206 r_rigid_bond_restr 4.077 r_mcangle_it 2.446 r_scbond_it 2.213 r_mcbond_it 1.991
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 52.543 r_dihedral_angle_2_deg 39.644 r_dihedral_angle_3_deg 19.255 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_1_deg 5.683 r_long_range_B_refined 4.206 r_rigid_bond_restr 4.077 r_mcangle_it 2.446 r_scbond_it 2.213 r_mcbond_it 1.991 r_angle_refined_deg 1.167 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6750 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction PHENIX phasing