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Crystal Structure of the Heterodimeric HIF-1a:ARNT Complex with HRE DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZP4 PDB entry 4ZP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 100 mM MES, pH 6.0, 100 mM calcium acetate, 15% PEG400
Crystal Properties Matthews coefficient Solvent content 2.82 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.735 α = 90 b = 66.735 β = 90 c = 243.644 γ = 90
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 315r 2014-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.9 50 99.1 0.045 0.052 0.027 11.2 3.8 9620 204.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 3.97 100 0.79 0.918 0.465 0.609 3.9 477
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entry 4ZP4 3.902 29.845 1.37 9578 962 99.3 0.2721 0.2645 0.2753 0.341 0.3451 194.6663
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_dihedral_angle_d 21.056 f_angle_d 0.843 f_chiral_restr 0.033 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4187 Nucleic Acid Atoms 855 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction SCALEPACK data scaling CORELS refinement