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Low pH structure of the Rieske protein from Thermus thermophilus at 2.1 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NYK Protein A of 1NYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.21 298 PEG 8000, Na Cacodylate, Calcium acetate, Pr(acetate)3, pH 6.21, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.152 α = 90 b = 58.512 β = 90 c = 58.798 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 IMAGE PLATE RIGAKU RAXIS HTC Mirrors 2008-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 58.8 99.7 0.088 4.5 23456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.099 2.154 99.8 0.529 4.4 2311
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT Protein A of 1NYK 2.1 58.8 23456 22217 1205 99.61 0.20072 0.20072 0.19806 0.1977 0.24601 0.2432 RANDOM 37.758
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] 0.43 -0.48 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.266 r_dihedral_angle_3_deg 16.693 r_dihedral_angle_4_deg 14.699 r_dihedral_angle_1_deg 6.876 r_scangle_it 4.166 r_scbond_it 2.623 r_angle_refined_deg 1.862 r_mcangle_it 1.759 r_mcbond_it 1.079 r_metal_ion_refined 0.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.266 r_dihedral_angle_3_deg 16.693 r_dihedral_angle_4_deg 14.699 r_dihedral_angle_1_deg 6.876 r_scangle_it 4.166 r_scbond_it 2.623 r_angle_refined_deg 1.862 r_mcangle_it 1.759 r_mcbond_it 1.079 r_metal_ion_refined 0.436 r_symmetry_hbond_refined 0.33 r_symmetry_vdw_refined 0.324 r_nbtor_refined 0.313 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.117 r_symmetry_metal_ion_refined 0.072 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling