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GephE in complex with Para-Phenyl crosslinked Glycine receptor beta subunit derived dimeric peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.2 M calcium acetate, 0.1M sodium acetate pH 4.5, 20-30% 2-methyl 2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.44 α = 90 b = 99.21 β = 90 c = 112.49 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS 6M 2014-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 56.2 100 0.09 10 5.9 33407
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.576 2.5 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FU3 2 20 31672 1688 99.81 0.17145 0.16851 0.22563 0.2228 RANDOM 48.437
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] 0.5 -0.29 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_4_deg 19.899 r_dihedral_angle_3_deg 16.435 r_long_range_B_refined 9.47 r_long_range_B_other 9.47 r_dihedral_angle_1_deg 6.778 r_scangle_other 6.04 r_mcangle_it 5.089 r_mcangle_other 5.088 r_scbond_it 4.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_4_deg 19.899 r_dihedral_angle_3_deg 16.435 r_long_range_B_refined 9.47 r_long_range_B_other 9.47 r_dihedral_angle_1_deg 6.778 r_scangle_other 6.04 r_mcangle_it 5.089 r_mcangle_other 5.088 r_scbond_it 4.007 r_scbond_other 4.007 r_mcbond_other 3.429 r_mcbond_it 3.428 r_angle_refined_deg 1.706 r_angle_other_deg 0.856 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3330 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing