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Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with palonosetron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM sodium 265 citrate, 100 mM bis tris propane pH 8.5, and 20% (w/v) PEG3350.
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.215 α = 90 b = 137.051 β = 93.78 c = 131.249 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 300K 2004-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.34 130.96 99.2 8.9 4.5 106052
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 2.34 2.47 94.5 0.845 0.598 1.6 4.4
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 2yme 2.34 130.96 100742 5294 98.82 0.2192 0.2179 0.2256 0.245 0.2539 RANDOM 55.902
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] -0.76 2.23 0.45 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.352 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_1_deg 6.754 r_mcangle_it 4.174 r_mcbond_it 2.921 r_mcbond_other 2.921 r_angle_refined_deg 1.819 r_angle_other_deg 1.005 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.352 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_1_deg 6.754 r_mcangle_it 4.174 r_mcbond_it 2.921 r_mcbond_other 2.921 r_angle_refined_deg 1.819 r_angle_other_deg 1.005 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16400 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling MOLREP phasing