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X-ray structure of the mambaquaretin-1, a selective antagonist of the vasopressin type 2 receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Protein: 7 mg/mL in 50mM sodium Acetate pH 5.5
Precipitant: 36% MPEG 2K, 0.45 M NaCl, 0.9 M KSCN, 0.1 M imidazole HCl, pH 7.5.
Cryoprotectant: 5 % diethylene glycol, 5 % ethylene glycol, 5 % MPD, 5 % glycerol, 5 % 1,2-propanediol, 5 % DMSO, 18% MPEG-2K, 100 mM linear mixed buffer 1: sodium acetate,
ADA, and bicine, 20% at pH 4 and 80% at pH 10.
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.84 α = 90 b = 63.84 β = 90 c = 32.96 γ = 90
Symmetry Space Group P 4 21 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 MIRRORS 2012-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976251 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.06 45.14 99.9 0.08 0.078 1 19.36 23.75 31490 -3 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.06 1.09 99.3 2.84 0.618 1.22 19.16
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1B0C 1.06 45.14 29915 1575 99.9 0.13195 0.13067 0.1317 0.15574 0.1552 RANDOM 19.648
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] 0.08 0.08 -0.16
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.975 r_dihedral_angle_2_deg 28.483 r_dihedral_angle_4_deg 18.121 r_dihedral_angle_3_deg 14.822 r_sphericity_bonded 12.152 r_dihedral_angle_1_deg 6.756 r_rigid_bond_restr 6.636 r_long_range_B_refined 6.383 r_long_range_B_other 5.299 r_scbond_it 3.377
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.975 r_dihedral_angle_2_deg 28.483 r_dihedral_angle_4_deg 18.121 r_dihedral_angle_3_deg 14.822 r_sphericity_bonded 12.152 r_dihedral_angle_1_deg 6.756 r_rigid_bond_restr 6.636 r_long_range_B_refined 6.383 r_long_range_B_other 5.299 r_scbond_it 3.377 r_scbond_other 3.358 r_scangle_other 3.317 r_angle_refined_deg 2.709 r_mcangle_it 2.057 r_mcangle_other 2.054 r_mcbond_it 1.849 r_mcbond_other 1.615 r_angle_other_deg 1.38 r_chiral_restr 0.134 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.013 r_gen_planes_other 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 448 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building