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Basic membrane protein D in complex with a nucleoside analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein solution (19 mg/ml): 44 mM Tris, pH 8.0; 4 % (v/v) DMSO; 6.3 mM triciribine
Well solution: 0.2 M lithium sulfate, 0.1 M phosphate/citrate pH 4.2, 20 % (w/v) PEG 1000
Sitting drop: 150 nl of protein solution, 50 nl of well solution.
Cryo solution: PEG 400 was added to the drop to a final concentration of 10 % (v/v).
Crystal Properties Matthews coefficient Solvent content 2.18 43.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.57 α = 90.797 b = 57.43 β = 108.443 c = 67.16 γ = 102.371
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 EIGER X 4M 2024-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 19.86 99.6 0.267 0.297 0.129 0.993 7.6 10 39513
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) 2 2.05 99.6 2.185 2.526 1.252 0.339 1.3 8.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 19.86 39512 2031 99.624 0.19 0.1874 0.188 0.2432 0.2443 39.442
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] -1.262 0.196 -0.231 0.854 0.317 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.349 r_dihedral_angle_6_deg 15.192 r_dihedral_angle_2_deg 14.214 r_lrange_other 8.054 r_lrange_it 8.047 r_dihedral_angle_1_deg 7.637 r_scangle_it 6.786 r_scangle_other 6.785 r_scbond_it 4.78 r_scbond_other 4.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.349 r_dihedral_angle_6_deg 15.192 r_dihedral_angle_2_deg 14.214 r_lrange_other 8.054 r_lrange_it 8.047 r_dihedral_angle_1_deg 7.637 r_scangle_it 6.786 r_scangle_other 6.785 r_scbond_it 4.78 r_scbond_other 4.779 r_mcangle_it 4.438 r_mcangle_other 4.438 r_mcbond_it 3.191 r_mcbond_other 3.19 r_angle_refined_deg 2.395 r_dihedral_angle_other_2_deg 1.8 r_angle_other_deg 0.828 r_symmetry_xyhbond_nbd_other 0.396 r_symmetry_xyhbond_nbd_refined 0.299 r_xyhbond_nbd_refined 0.254 r_nbd_refined 0.224 r_nbd_other 0.223 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.196 r_symmetry_nbd_refined 0.17 r_chiral_restr 0.123 r_symmetry_nbtor_other 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4793 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 84
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement