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Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FWX PDB entry 1FWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 16 % PEG 6000, 0.2 M imidazole/malate buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.577 α = 111.45 b = 106.453 β = 107.22 c = 130.876 γ = 90.72
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 PSI PILATUS 6M mirrors 2010-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.24 95.05 94.6 0.09 12.8 3.8 205995 194872 2 2
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 PDB entry 1FWX 2.24 95 194872 10299 93.27 0.17584 0.17317 0.1744 0.22655 0.2261 RANDOM 20.219
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] 0.13 -0.09 -0.03 -0.13 -0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.771 r_dihedral_angle_4_deg 16.969 r_dihedral_angle_3_deg 16.055 r_dihedral_angle_1_deg 7.045 r_scangle_it 2.539 r_scbond_it 1.556 r_angle_refined_deg 1.317 r_mcangle_it 0.909 r_mcbond_it 0.474 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.771 r_dihedral_angle_4_deg 16.969 r_dihedral_angle_3_deg 16.055 r_dihedral_angle_1_deg 7.045 r_scangle_it 2.539 r_scbond_it 1.556 r_angle_refined_deg 1.317 r_mcangle_it 0.909 r_mcbond_it 0.474 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36623 Nucleic Acid Atoms Solvent Atoms 2628 Heterogen Atoms 124
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling