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Basic membrane protein D in complex with cytidine
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 (~20 mg/ml): 50 mM Tris pH 8.0; 1 mg/ml hygromycin A
Well solution: 0.2 M CaCl2, 0.1 M Hepes pH 7.0, 22.5 % PEG6000
Seed stock from an earlier crystallization trial (may have contained very low levels of cytidine): 0.2 M CaCl2, 0.1M Tris pH 8.4, 22.5 % w/v PEG6000
Sitting drops: 1000 nl of protein solution, 660 nl of well solution and 330 nl of seed stock.
Cryo solution: 50% MPD was added to the drop to a final concentration of 16% (v/v).
Crystal Properties Matthews coefficient Solvent content 1.98 37.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.28 α = 81.06 b = 57.53 β = 71.367 c = 67.617 γ = 77.14
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 EIGER2 X 9M 2023-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873130 ESRF ID23-2
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 1.2 50 88.2 0.075 0.084 0.036 0.997 9.6 5.3 165512
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 1.2 1.22 51.3 1.523 1.688 0.72 0.39 1.1 5.3
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 1.2 44.07 165512 8201 88.19 0.139 0.1373 0.1347 0.1755 0.1745 25.319
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] 0.656 0.816 -1.069 -0.237 -1.026 -0.609
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.243 r_lrange_other 18.825 r_scangle_it 15.593 r_scangle_other 15.591 r_dihedral_angle_6_deg 14.967 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_2_deg 11.981 r_mcangle_other 11.491 r_mcangle_it 11.489 r_scbond_it 11.13
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.243 r_lrange_other 18.825 r_scangle_it 15.593 r_scangle_other 15.591 r_dihedral_angle_6_deg 14.967 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_2_deg 11.981 r_mcangle_other 11.491 r_mcangle_it 11.489 r_scbond_it 11.13 r_scbond_other 11.128 r_mcbond_it 9.769 r_mcbond_other 9.755 r_rigid_bond_restr 7.267 r_dihedral_angle_1_deg 6.159 r_angle_refined_deg 2.039 r_angle_other_deg 0.741 r_nbd_refined 0.225 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.185 r_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.132 r_chiral_restr 0.124 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 r_dihedral_angle_other_2_deg 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4784 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 57
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement