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The Crystal Structure of Water-forming NAD(P)H Oxidase from Lactobacillus sanfranciscensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8W PDB ENTRY 1F8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 10 MG/ML PROTEIN, 100MM HEPES PH 7.0, 18% W/V PEG 4000, 8% V/V 2-PROPANOL, 20 MM DITHIOTHREITOL
Crystal Properties Matthews coefficient Solvent content 2.3 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.636 α = 90 b = 92.644 β = 90 c = 163.465 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2004-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-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 1.8 46.4 96.1 0.1 29 8.5 81507 2
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 1.8 1.85 73.8 0.49 1.9 4.1
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 1F8W 1.8 81.65 77370 4054 96.1 0.18 0.178 0.1889 0.223 0.2325 RANDOM 24.07
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] 2.09 -0.11 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.542 r_scangle_it 3.935 r_scbond_it 2.378 r_angle_refined_deg 1.542 r_mcangle_it 1.492 r_angle_other_deg 0.992 r_mcbond_it 0.81 r_symmetry_vdw_other 0.291 r_symmetry_hbond_refined 0.251 r_nbd_other 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.542 r_scangle_it 3.935 r_scbond_it 2.378 r_angle_refined_deg 1.542 r_mcangle_it 1.492 r_angle_other_deg 0.992 r_mcbond_it 0.81 r_symmetry_vdw_other 0.291 r_symmetry_hbond_refined 0.251 r_nbd_other 0.249 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.097 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6937 Nucleic Acid Atoms Solvent Atoms 708 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing