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Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer in complex with adrenomedullin 2/intermedin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 13% v/v PEG 3,350
0.1 M Na cacodylate, pH 6.5
0.15 M DL-malic acid
Crystal Properties Matthews coefficient Solvent content 2.58 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.295 α = 90 b = 106.041 β = 122.53 c = 136.911 γ = 90
Symmetry Space Group C 1 2 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 CCD RAYONIX MX300-HS 2017-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.05 50 98.9 0.062 0.067 0.024 8.5 7.5 128678
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 2.05 2.09 91 1.202 1.296 0.48 0.759 6.5
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 4rwg 2.05 45.64 121708 6603 98.63 0.1954 0.194 0.1996 0.2228 0.2238 RANDOM 66.542
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] 1.53 0.34 1.81 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.869 r_dihedral_angle_4_deg 19.761 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 5.807 r_angle_refined_deg 1.519 r_angle_other_deg 0.993 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.869 r_dihedral_angle_4_deg 19.761 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 5.807 r_angle_refined_deg 1.519 r_angle_other_deg 0.993 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13525 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 76
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing