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HOXB13-homodimer bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 24 % PEG 1500 MME, 0.15M potassium chloride, 0.05M Tris-HCl buffer, 2%PEG 400
Crystal Properties Matthews coefficient Solvent content 3.3 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.779 α = 90 b = 116.779 β = 90 c = 118.057 γ = 90
Symmetry Space Group P 43 21 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 PIXEL PSI PILATUS 6M 2014-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.91 59.03 99.5 0.134 0.05 0.995 8.6 7.5 18396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.91 3.07 96.9 4.116 1.458 0.323 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 30 16051 840 99.82 0.25635 0.2539 0.2803 0.30432 0.3196 RANDOM 116.374
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] -4.38 -4.38 8.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.723 r_dihedral_angle_1_deg 27.606 r_dihedral_angle_3_deg 21.561 r_long_range_B_refined 18.444 r_long_range_B_other 18.444 r_dihedral_angle_4_deg 17.415 r_mcangle_other 14.315 r_mcangle_it 14.312 r_scangle_other 14.158 r_mcbond_it 8.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.723 r_dihedral_angle_1_deg 27.606 r_dihedral_angle_3_deg 21.561 r_long_range_B_refined 18.444 r_long_range_B_other 18.444 r_dihedral_angle_4_deg 17.415 r_mcangle_other 14.315 r_mcangle_it 14.312 r_scangle_other 14.158 r_mcbond_it 8.911 r_mcbond_other 8.874 r_scbond_it 8.731 r_scbond_other 8.73 r_angle_refined_deg 1.408 r_angle_other_deg 1.278 r_chiral_restr 0.178 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3009 Nucleic Acid Atoms 2198 Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing