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Phage-Selected Homeodomain Bound to Unmodified DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HDD PDB ENTRY 2HDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Well: 20% PEG400, 100mM NH4OAc
Drop: 0.5mM DNA Protein Complex, 0.55M NH4OAc, 3.5mM bis-Tris-Propane, 10% PEG-400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.24 61.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.097 α = 90 b = 45.025 β = 118.41 c = 73.081 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 210 KOHZU: Double Crystal Si(111) 2005-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11588 ALS 8.3.1
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 1.8 50 84.3 0.035 13.6 3.7 28750
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) 1 1.8 1.86 33.7 0.391 2.3
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-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 2HDD 1.9 32.48 23285 1710 86.29 0.22535 0.22308 0.2129 0.25693 0.2479 RANDOM 42.351
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] -0.96 -0.01 0.4 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.522 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_1_deg 4.613 r_scangle_it 2.667 r_scbond_it 1.726 r_angle_refined_deg 1.702 r_mcangle_it 1.132 r_mcbond_it 0.69 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.522 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_1_deg 4.613 r_scangle_it 2.667 r_scbond_it 1.726 r_angle_refined_deg 1.702 r_mcangle_it 1.132 r_mcbond_it 0.69 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.185 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.091 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 950 Nucleic Acid Atoms 855 Solvent Atoms 129 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling CNS phasing