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Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QGQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 10 291 Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 20 mg/ml, 5 DTT, 10 equivalents FeCl3 and Na2S. Reservoir solution: 100 mM CAPS pH 10.0, 40% PEG 4000, 100 mM Sodium thiosulfate, MICROBATCH UNDER OIL, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.721 α = 90 b = 86.948 β = 90 c = 172.795 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors 2011-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.3 41.45 92.4 0.136 0.091 13.71 4.9 63690 14135 85.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.42 81.4 0.407 0.368 2.34 4.1
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 (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 2QGQ 3.3 41.46 14135 11747 1210 83.1 0.245 0.245 0.229 0.296 0.2863 RANDOM 101.7
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] -16.78 -32.01 48.79
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_angle_deg 1.1 c_improper_angle_d 0.69 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_angle_deg 1.1 c_improper_angle_d 0.69 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6808 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing