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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1 microL of 10 mg ml-1 protein in 10 mM Tris pH 8.0 with 1 microL of 100 mM Na-acetate pH 4.75, 200 mM (NH4)2SO4, 31 % (w/v) PEG 3350, 2% (w/v) glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.22 α = 103.13 b = 54.49 β = 95.21 c = 104.872 γ = 90.01
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 Double Si(111) monoichromation 2005-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.488 SRS PX10.1
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 2.35 101.687 96.4 0.105 0.105 4.1 2.2 34657 34657
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) 2.35 2.48 93.3 0.144 0.144 4.1 2.2
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 2OX5 2.35 50 34657 32903 1754 96.38 0.19659 0.19394 0.1947 0.24433 0.243 RANDOM 14.633
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] 0.58 0.12 0.69 -0.12 -0.08 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.275 r_dihedral_angle_3_deg 17.221 r_dihedral_angle_4_deg 14.87 r_dihedral_angle_1_deg 12.656 r_scangle_it 3.631 r_scbond_it 2.282 r_mcangle_it 1.407 r_angle_refined_deg 1.376 r_mcbond_it 0.802 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.275 r_dihedral_angle_3_deg 17.221 r_dihedral_angle_4_deg 14.87 r_dihedral_angle_1_deg 12.656 r_scangle_it 3.631 r_scbond_it 2.282 r_mcangle_it 1.407 r_angle_refined_deg 1.376 r_mcbond_it 0.802 r_nbtor_refined 0.298 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_refined 0.153 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6403 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 24
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOSFLM data reduction MOLREP phasing