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Crystal structure of NAD(P)H-flavin oxidoreductase from Helicobacter pylori
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 0.1M Na(OAC), 27% PEG2KMME, 5mM FMN, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.035 α = 90 b = 87.178 β = 90 c = 94.979 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 315 2005-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.89 50 99 0.087 45 5 18453 18268 -3
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 1.89 1.96 92.9 0.182 12.8 4.6 1685
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 47.51 17063 17063 919 99.66 0.17988 0.17988 0.17771 0.1771 0.22054 0.2202 RANDOM 18.295
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] 0.36 0.52 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.203 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_4_deg 10.819 r_dihedral_angle_1_deg 5.707 r_scangle_it 4.338 r_scbond_it 3.026 r_mcangle_it 1.541 r_mcbond_it 1.468 r_angle_refined_deg 1.422 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.203 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_4_deg 10.819 r_dihedral_angle_1_deg 5.707 r_scangle_it 4.338 r_scbond_it 3.026 r_mcangle_it 1.541 r_mcbond_it 1.468 r_angle_refined_deg 1.422 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.254 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 1595 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building