☰ Navigation Tabs
Structure of the oxygen-insensitive NAD(P)H-dependent nitroreductase NfsB_Ec F70A/F108Y in complex with FMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DS7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 Sodium chloride, sodium acetate trihydrate, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.22 α = 90 b = 95.59 β = 90 c = 112.31 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 ADSC QUANTUM 210r 2015-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 1.98 87.22 100 0.151 9.9 7.1 66067
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 1.98 2.03 100 0.814 2.5 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.98 72.79 62693 3293 99.95 0.17296 0.1706 0.1819 0.21912 0.2253 RANDOM 16.405
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] -0.04 0.99 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_4_deg 18.994 r_dihedral_angle_3_deg 14.081 r_dihedral_angle_1_deg 6.205 r_long_range_B_refined 5.371 r_long_range_B_other 5.371 r_scangle_other 2.953 r_mcangle_it 2.517 r_mcangle_other 2.517 r_scbond_it 1.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_4_deg 18.994 r_dihedral_angle_3_deg 14.081 r_dihedral_angle_1_deg 6.205 r_long_range_B_refined 5.371 r_long_range_B_other 5.371 r_scangle_other 2.953 r_mcangle_it 2.517 r_mcangle_other 2.517 r_scbond_it 1.891 r_scbond_other 1.891 r_angle_refined_deg 1.595 r_mcbond_it 1.568 r_mcbond_other 1.539 r_angle_other_deg 1.445 r_chiral_restr 0.079 r_bond_refined_d 0.01 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 6652 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing