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Crystal structure of the D55E mutant of the HupR receiver domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JK1 PDB ENTRY 2JK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 2.4 M NACL, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.0, 28% ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 3.74 67.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.782 α = 90 b = 81.782 β = 90 c = 61.046 γ = 120
Symmetry Space Group P 32 1 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 CCD ADSC CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.5 24.52 99 0.06 26.5 8.1 7797 2
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 2.5 2.6 99.9 0.34 6.4 8.3
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 2JK1 2.5 24.52 7797 399 99.78 0.22204 0.2207 0.2217 0.24714 0.2517 RANDOM 53.466
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] 2.51 1.25 2.51 -3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.397 r_dihedral_angle_4_deg 25.623 r_dihedral_angle_3_deg 21.088 r_dihedral_angle_1_deg 8.389 r_scangle_it 3.935 r_scbond_it 2.322 r_mcangle_it 1.797 r_angle_refined_deg 1.763 r_mcbond_it 1.044 r_symmetry_hbond_refined 0.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.397 r_dihedral_angle_4_deg 25.623 r_dihedral_angle_3_deg 21.088 r_dihedral_angle_1_deg 8.389 r_scangle_it 3.935 r_scbond_it 2.322 r_mcangle_it 1.797 r_angle_refined_deg 1.763 r_mcbond_it 1.044 r_symmetry_hbond_refined 0.551 r_nbtor_refined 0.316 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.114 r_bond_refined_d 0.017 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1062 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing