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Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DUX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 PEG 4000, Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.16 α = 90 b = 71.476 β = 113.45 c = 39.136 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 113 IMAGE PLATE RIGAKU RAXIS IV Osmic Max-FLUX confocal 2004-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 35.9 94.7 0.082 17.1 3.74 11755 11176 25.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 85.4 0.23 6.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DUX 2 35.9 11799 11799 561 94.72 0.2049 0.20321 0.23889 0.2781 RANDOM 25.592
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] 3.12 -0.96 -2.84 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.841 r_dihedral_angle_4_deg 15.731 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_1_deg 5.223 r_scangle_it 1.817 r_angle_refined_deg 1.314 r_scbond_it 1.15 r_mcangle_it 1.052 r_mcbond_it 0.604 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.841 r_dihedral_angle_4_deg 15.731 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_1_deg 5.223 r_scangle_it 1.817 r_angle_refined_deg 1.314 r_scbond_it 1.15 r_mcangle_it 1.052 r_mcbond_it 0.604 r_nbtor_refined 0.299 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 759 Nucleic Acid Atoms 527 Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement