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Basic membrane protein D in complex with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 Well solution:
0.2 M CaCl2, 0.1 M sodium acetate pH 5.0, 20 % PEG6000
Crystal Properties Matthews coefficient Solvent content 1.98 37.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.23 α = 81.14 b = 57.68 β = 71.429 c = 67.606 γ = 77.108
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 2017-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 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 1.4 39.76 90.2 0.046 0.064 0.046 0.997 14.1 3.9 106776
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) 1.4 1.42 66.9 0.587 0.829 0.586 0.754 1.9 3.9
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 1.4 39.76 106776 5189 90.131 0.142 0.1403 0.1375 0.182 0.1789 19.698
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] 0.508 0.275 -0.556 -1.551 -0.133 0.791
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.609 r_dihedral_angle_6_deg 15.244 r_lrange_other 13.776 r_dihedral_angle_2_deg 13.163 r_dihedral_angle_3_deg 12.124 r_scangle_it 9.54 r_scangle_other 9.538 r_mcangle_other 6.892 r_mcangle_it 6.889 r_scbond_other 6.69
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.609 r_dihedral_angle_6_deg 15.244 r_lrange_other 13.776 r_dihedral_angle_2_deg 13.163 r_dihedral_angle_3_deg 12.124 r_scangle_it 9.54 r_scangle_other 9.538 r_mcangle_other 6.892 r_mcangle_it 6.889 r_scbond_other 6.69 r_scbond_it 6.689 r_dihedral_angle_1_deg 6.173 r_mcbond_it 4.837 r_mcbond_other 4.822 r_rigid_bond_restr 3.654 r_angle_refined_deg 1.748 r_angle_other_deg 0.641 r_symmetry_xyhbond_nbd_other 0.262 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.181 r_nbd_other 0.149 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.081 r_dihedral_angle_other_2_deg 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 866 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing REFMAC refinement