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Structure of thermostable DNA-binding HU protein from micoplasma Spiroplasma melliferum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 0.1M TRIS, 35% PEG400, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57 α = 90 b = 39.01 β = 108.36 c = 38.78 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 MAR CCD 165 mm 2012-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.984 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.4 31.64 95.4 0.049 0.058 0.03 0.997 13.5 3.6 15292
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 1.4 1.42 96.8 0.279 3.5
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 1HUU 1.4 31.64 14567 724 95.29 0.1815 0.18 0.1827 0.2113 0.2119 RANDOM 17.707
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] 0.77 -0.19 -0.02 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.801 r_dihedral_angle_3_deg 16.053 r_dihedral_angle_4_deg 14.564 r_dihedral_angle_1_deg 6.84 r_scbond_it 2.418 r_mcangle_it 2.409 r_angle_refined_deg 2.229 r_mcbond_it 1.708 r_chiral_restr 0.123 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.801 r_dihedral_angle_3_deg 16.053 r_dihedral_angle_4_deg 14.564 r_dihedral_angle_1_deg 6.84 r_scbond_it 2.418 r_mcangle_it 2.409 r_angle_refined_deg 2.229 r_mcbond_it 1.708 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 704 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 1
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction BALBES phasing