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Complex crystal structure of hydroxylamine oxidoreductase and NE1300 from Nitrosomonas europaea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FGJ Monomer of PDB ID: 1FGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 292 0.1 M potassium nitrate, 0.1 M MES pH 7.5 and 46%(v/v) PEG 400, VAPOR DIFFUSION, temperature 292K 2 VAPOR DIFFUSION 7.5 292 0.1 M potassium nitrate, 0.1 M MES pH 7.5 and 46%(v/v) PEG 400, VAPOR DIFFUSION, temperature 292K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.731 α = 90 b = 142.618 β = 90 c = 107.376 γ = 90
Symmetry Space Group P 21 21 2
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 315 Mirror 2009-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97948 APS 19-ID
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 2.1 50 86.7 0.127 9.554 4.6 125826 109103 -3 32.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 69.3 0.574 2.036 3.9 4298
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 Monomer of PDB ID: 1FGJ 2.1 42.89 119593 95555 5071 79.9 0.16701 0.16701 0.16493 0.166 0.20583 0.2061 RANDOM 37.348
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] -1.75 -0.15 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.194 r_dihedral_angle_4_deg 19.875 r_dihedral_angle_3_deg 17.487 r_dihedral_angle_1_deg 6.466 r_scangle_it 4.39 r_scbond_it 3.202 r_angle_refined_deg 2.102 r_mcangle_it 1.781 r_mcbond_it 1.037 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.194 r_dihedral_angle_4_deg 19.875 r_dihedral_angle_3_deg 17.487 r_dihedral_angle_1_deg 6.466 r_scangle_it 4.39 r_scbond_it 3.202 r_angle_refined_deg 2.102 r_mcangle_it 1.781 r_mcbond_it 1.037 r_chiral_restr 0.128 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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 13125 Nucleic Acid Atoms Solvent Atoms 785 Heterogen Atoms 1279
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling