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The SoxYZ Complex of Paracoccus pantotrophus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OX5 PDB ENTRY 2OX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 2 microl of protein at 10 mg/ml in 10 mM Tris-HCl pH 8, 5 mM DTT and 2 microl of 31-32 % (w/v) PEG 3350, 100 mM sodium acetate pH 4.75, 200 mM NH4SO4 and 2 % (v/v) glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.828 α = 90 b = 54.717 β = 98.68 c = 77.677 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 ADSC QUANTUM 4 Diamond (111), Laue geometry, 150 microns thin 2003-11-17 M SINGLE WAVELENGTH 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1,2 1.4 102.229 97.9 0.042 0.042 7.6 1.9 164928 164928 15.9
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) 1.4 1.48 96.7 0.395 0.395 1.7 1.9 23687
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 PDB ENTRY 2OX5 1.4 50 164923 164923 8301 97.59 0.17 0.17 0.168 0.1663 0.194 0.1926 RANDOM 19.941
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] -0.07 0.15 0.24 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.801 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_3_deg 11.817 r_dihedral_angle_1_deg 6.259 r_scangle_it 4.652 r_scbond_it 3.236 r_mcangle_it 2.202 r_mcbond_it 1.513 r_angle_refined_deg 1.402 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.801 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_3_deg 11.817 r_dihedral_angle_1_deg 6.259 r_scangle_it 4.652 r_scbond_it 3.236 r_mcangle_it 2.202 r_mcbond_it 1.513 r_angle_refined_deg 1.402 r_nbtor_refined 0.305 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.206 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6309 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms 31
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction MOLREP phasing