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DNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HCQ PDB ENTRY 1HCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN/DNA COMPLEX CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION METHOD AT 27
DEGREES CELSIUS. THE RESEVOIR CONTAINS 50 MM MORPHOLINO-SULFONIC ACID PH7.0,
250MM AMMONIUM CHLORIDE, 30 % PEG 4000, 5 MM DTT. THE DROPS CONTAINED A 1:1
RATIO OF PROTEIN-COMPLEX TO RESEVOIR.
Crystal Properties Matthews coefficient Solvent content 2.4 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.42 α = 90 b = 34.24 β = 109.13 c = 56.26 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 IMAGE PLATE MARRESEARCH MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B NSLS X12B
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 2.7 18 95 0.073 14.5 2.3 5200 3 80.3
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) 2.7 2.8 96.9 0.368 3.1
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-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 1HCQ 2.7 18 5200 568 95 0.219 0.2237 0.295 0.3018 RANDOM 32.8
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 c_dihedral_angle_d 21.6 c_scangle_it 6.34 c_mcangle_it 4.83 c_scbond_it 4.36 c_mcbond_it 3.06 c_angle_deg 2.4 c_improper_angle_d 1.78 c_bond_d 0.016 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 6.34 c_mcangle_it 4.83 c_scbond_it 4.36 c_mcbond_it 3.06 c_angle_deg 2.4 c_improper_angle_d 1.78 c_bond_d 0.016 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 690 Nucleic Acid Atoms 650 Solvent Atoms 38 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building MLPHARE phasing CNS refinement X-PLOR phasing