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Crystal structure of EmrR homolog from hyperthermophilic archaea Sulfolobus tokodaii strain7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 21% PEG 2000 monomethyl ethyl, 0.1M Tris-HCl, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.114 α = 90 b = 46.114 β = 90 c = 140.257 γ = 90
Symmetry Space Group P 41 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 95 CCD ADSC QUANTUM 315 2004-05-29 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000, 0.9841, 0.9794, 0.9792 Photon Factory BL-5A
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 1.45 20 99.5 0.072 16 10.4 27739
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 1.45 1.5 99 0.223 5.5
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 (All) 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 MAD THROUGHOUT 1.45 20 26266 1394 99.54 0.22333 0.22333 0.22252 0.2302 0.239 0.2514 RANDOM 19.653
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.251 r_scangle_it 4.545 r_scbond_it 2.696 r_mcangle_it 1.692 r_angle_refined_deg 1.558 r_mcbond_it 0.971 r_angle_other_deg 0.856 r_symmetry_vdw_other 0.272 r_nbd_other 0.238 r_nbd_refined 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.251 r_scangle_it 4.545 r_scbond_it 2.696 r_mcangle_it 1.692 r_angle_refined_deg 1.558 r_mcbond_it 0.971 r_angle_other_deg 0.856 r_symmetry_vdw_other 0.272 r_nbd_other 0.238 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.092 r_nbtor_other 0.082 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1132 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection