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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 NaAcetate pH 5.0, 20 % PEG6000
Seed stock from an earlier crystallization trial (may have contained very low levels of cytidine):
0.2 M CaCl2, 0.1M Tris pH 8.0, 22.5 % w/v PEG6000
Sitting drops:
90 nl of protein solution, 90 nl of well solution and 30 nl of seed stock.
Cryo solution:
50% MPD were added to the drop to a final concentration of 16% (v/v).
Crystal Properties Matthews coefficient Solvent content 1.98 37.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.39 α = 90.963 b = 57.49 β = 108.595 c = 67.59 γ = 102.719
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 1.25 40.18 97 0.112 0.14 0.083 0.995 7.1 5 161460
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) 1.25 1.27 82.2 1.611 2.031 1.211 0.337 1.5 4.4
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 1.25 40.18 161447 8094 97.019 0.13 0.1283 0.1287 0.1644 0.1655 21.372
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] 2.388 0.953 -0.19 -0.316 0.031 -1.859
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.902 r_lrange_other 15.795 r_dihedral_angle_6_deg 15.725 r_dihedral_angle_3_deg 12.434 r_scangle_it 11.529 r_scangle_other 11.465 r_mcangle_other 8.226 r_mcangle_it 8.222 r_scbond_it 7.912 r_scbond_other 7.879
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.902 r_lrange_other 15.795 r_dihedral_angle_6_deg 15.725 r_dihedral_angle_3_deg 12.434 r_scangle_it 11.529 r_scangle_other 11.465 r_mcangle_other 8.226 r_mcangle_it 8.222 r_scbond_it 7.912 r_scbond_other 7.879 r_dihedral_angle_2_deg 6.618 r_dihedral_angle_1_deg 5.913 r_mcbond_it 5.668 r_mcbond_other 5.62 r_rigid_bond_restr 3.994 r_angle_refined_deg 1.715 r_angle_other_deg 0.631 r_symmetry_nbd_refined 0.268 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.183 r_nbd_other 0.174 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.01 r_dihedral_angle_other_2_deg 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4784 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 64
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement