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Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BP3 FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D. experimental model PDB 1F6F FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D. experimental model PDB 1RW5 FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D. experimental model PDB 1N9D FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 297 3.5M Sodium Chloride, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.41 63.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.35 α = 90 b = 125.35 β = 90 c = 69.82 γ = 120
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 MARMOSAIC 225 mm CCD 2007-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 20 99.8 0.083 22.46 11.2 21763 21797 -3 -3 46.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.56 100 0.501 5.5 11.2 21797
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D. 2.5 20 21717 20629 1088 99.87 0.221 0.221 0.218 0.2166 0.295 0.2931 RANDOM 46.307
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] -2.48 -1.24 -2.48 3.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 22.244 r_dihedral_angle_4_deg 20.394 r_dihedral_angle_1_deg 8.69 r_scangle_it 4.035 r_scbond_it 2.465 r_angle_refined_deg 2.013 r_mcangle_it 1.782 r_mcbond_it 0.964 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 22.244 r_dihedral_angle_4_deg 20.394 r_dihedral_angle_1_deg 8.69 r_scangle_it 4.035 r_scbond_it 2.465 r_angle_refined_deg 2.013 r_mcangle_it 1.782 r_mcbond_it 0.964 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2945 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing