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X-ray structure of ERRalpha LBD in complex with a PGC-1alpha peptide at 2.5A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KV6 PDB ENTRY 1KV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 NaCl, KI, PEG4000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.3 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.999 α = 90 b = 109.999 β = 90 c = 104.671 γ = 120
Symmetry Space Group P 65 2 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 MARRESEARCH 2003-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.8000 SLS X06SA
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 94.7 0.099 27.5 12.3 12704 12704 50.9
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 2.59 91.5 0.41 2.8 1186
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 PDB ENTRY 1KV6 2.5 20 12060 12060 625 94.8 0.2165 0.2165 0.21491 0.2093 0.2473 0.2318 RANDOM 38.271
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] -0.59 -0.3 -0.59 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.355 r_scangle_it 3.798 r_scbond_it 2.104 r_mcangle_it 1.599 r_angle_refined_deg 1.447 r_angle_other_deg 0.953 r_mcbond_it 0.83 r_symmetry_hbond_refined 0.339 r_symmetry_vdw_other 0.28 r_nbd_other 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.355 r_scangle_it 3.798 r_scbond_it 2.104 r_mcangle_it 1.599 r_angle_refined_deg 1.447 r_angle_other_deg 0.953 r_mcbond_it 0.83 r_symmetry_hbond_refined 0.339 r_symmetry_vdw_other 0.28 r_nbd_other 0.222 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.167 r_nbtor_other 0.081 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1741 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing