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Crystal structure of sigma-2 receptor with zervimesine (CT1812)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5 293 0.1 M trisodium citrate pH 5.0; 0.2 M sodium chloride; 32% v/v PEG 300
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.012 α = 90 b = 54.44 β = 94.824 c = 92.755 γ = 90
Symmetry Space Group P 1 21 1
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 CdTe 16M 2025-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.74 71 100 0.99 7.1 6.8 18816
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.79 0.53
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.74 71 18804 1009 99.915 0.236 0.235 0.2408 0.257 0.2621 RANDOM 54.353
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] 0.074 1.828 -1.651 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.426 r_dihedral_angle_6_deg 13.548 r_dihedral_angle_other_3_deg 10.088 r_dihedral_angle_1_deg 6.383 r_lrange_it 5.937 r_lrange_other 5.937 r_mcangle_it 3.89 r_mcangle_other 3.889 r_scangle_it 3.569 r_scangle_other 3.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.426 r_dihedral_angle_6_deg 13.548 r_dihedral_angle_other_3_deg 10.088 r_dihedral_angle_1_deg 6.383 r_lrange_it 5.937 r_lrange_other 5.937 r_mcangle_it 3.89 r_mcangle_other 3.889 r_scangle_it 3.569 r_scangle_other 3.569 r_mcbond_it 2.285 r_mcbond_other 2.284 r_scbond_it 2.043 r_scbond_other 2.043 r_angle_refined_deg 1.275 r_dihedral_angle_2_deg 1.251 r_angle_other_deg 0.493 r_nbtor_refined 0.184 r_nbd_refined 0.182 r_symmetry_nbd_other 0.163 r_nbd_other 0.142 r_xyhbond_nbd_refined 0.116 r_symmetry_nbd_refined 0.09 r_symmetry_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.067 r_chiral_restr 0.059 r_ncsr_local_group_2 0.047 r_ncsr_local_group_4 0.045 r_ncsr_local_group_6 0.04 r_ncsr_local_group_3 0.037 r_ncsr_local_group_1 0.035 r_ncsr_local_group_5 0.03 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5464 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling TRUNCATE data processing Coot model building PHASER phasing