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Crystal structure of the extracellular domain of human corticotropin releasing factor receptor type 1 (CRFR1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C4M pdb entry 3C4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.7 293 NaCl, sucrose, sodium acetate, pH 4.7, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.35 71.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.018 α = 90 b = 112.018 β = 90 c = 145.786 γ = 90
Symmetry Space Group P 41 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97872 APS 21-ID-D
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 2.75 50 98.4 0.059 33.26 13.8 24253 -3
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 2.75 2.85 90.2 0.573 2.99
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 pdb entry 3C4M 2.76 50 22955 1238 98.33 0.209 0.207 0.2087 0.24 0.2408 RANDOM 93.281
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] -1.36 -1.36 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.088 r_dihedral_angle_4_deg 20.392 r_dihedral_angle_3_deg 17.636 r_dihedral_angle_1_deg 5.814 r_scangle_it 1.834 r_angle_refined_deg 1.233 r_scbond_it 1.171 r_mcangle_it 0.78 r_mcbond_it 0.46 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.088 r_dihedral_angle_4_deg 20.392 r_dihedral_angle_3_deg 17.636 r_dihedral_angle_1_deg 5.814 r_scangle_it 1.834 r_angle_refined_deg 1.233 r_scbond_it 1.171 r_mcangle_it 0.78 r_mcbond_it 0.46 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3539 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling