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SF-1 LBD bound by phosphatidylcholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YMT PDb entry 1YMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M sodium cacodylate, 20% PEG 3350, 0.2 M sodium acetate, 2 mM TCEP, 10% xylitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.895 α = 90 b = 67.228 β = 90 c = 82.689 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 mirrors 2005-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 25 95.86 0.07 0.07 15.1 3.7 13803 13232 26.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 89.5 0.24 0.24 3.3 2.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDb entry 1YMT 2.2 23.76 0.06 13803 13232 399 95.9 0.182 0.18 0.1795 0.241 0.234
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]
RMS Deviations Key Refinement Restraint Deviation f_angle_d 1.006 f_bond_d 0.008 f_dihedral_angle_d f_chiral_restr f_plane_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1996 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing