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HU DNA-binding protein from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 293 Protein solutions of 14-18 mg/ml, Buffer: 0.2 M Na-formate, Precipitating agent: 20%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.464 α = 90 b = 38.432 β = 90 c = 44.861 γ = 90
Symmetry Space Group P 21 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 DECTRIS PILATUS 6M BIMORPH MIRRORS 2015-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97631 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.69 44.9 96.3 0.073 22.6 12 10742 20.4
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 1.69 1.74 59.6 0.51 3 7.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1B8Z 1.69 44.86 10208 534 96.28 0.20077 0.19776 0.25612 0.2586 RANDOM 31
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] 0.5 -1.01 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_3_deg 16.252 r_long_range_B_refined 7.472 r_long_range_B_other 7.4 r_dihedral_angle_1_deg 5.011 r_scangle_other 3.104 r_scbond_it 1.929 r_scbond_other 1.929 r_mcangle_other 1.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_3_deg 16.252 r_long_range_B_refined 7.472 r_long_range_B_other 7.4 r_dihedral_angle_1_deg 5.011 r_scangle_other 3.104 r_scbond_it 1.929 r_scbond_other 1.929 r_mcangle_other 1.593 r_mcangle_it 1.59 r_angle_refined_deg 1.477 r_mcbond_it 1.029 r_mcbond_other 1.013 r_angle_other_deg 0.759 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 644 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing