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Recombinant Pseudomonas stutzeri nitrous oxide reductase, form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M bis-tris propane buffer at pH 8.5, 0.1 M sodium formate, 0.1 M sodium chloride, and 25% (w/v) of a medium molecular weight (MMW) polyethylene glycol mixture (PEG 2K, 3350, 4K and 5K MME)
Crystal Properties Matthews coefficient Solvent content 35.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.916 α = 90 b = 73.372 β = 95.07 c = 136.342 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 2M 2016-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.36999 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.78 48.91 100 15.7 13 205189
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3SBQ 1.78 48.91 194905 10243 99.98 0.15876 0.157 0.1665 0.19225 0.2011 RANDOM 28.816
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] -0.59 0.33 0.04 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.325 r_dihedral_angle_4_deg 16.346 r_dihedral_angle_3_deg 13.89 r_dihedral_angle_1_deg 7.226 r_long_range_B_refined 5.769 r_long_range_B_other 5.74 r_scangle_other 4.372 r_scbond_it 2.849 r_scbond_other 2.838 r_mcangle_other 2.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.325 r_dihedral_angle_4_deg 16.346 r_dihedral_angle_3_deg 13.89 r_dihedral_angle_1_deg 7.226 r_long_range_B_refined 5.769 r_long_range_B_other 5.74 r_scangle_other 4.372 r_scbond_it 2.849 r_scbond_other 2.838 r_mcangle_other 2.803 r_mcangle_it 2.802 r_mcbond_it 2.004 r_mcbond_other 2.004 r_angle_refined_deg 1.946 r_angle_other_deg 0.95 r_chiral_restr 0.145 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18329 Nucleic Acid Atoms Solvent Atoms 1455 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing