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XiaF (FADH2) from Streptomyces sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1,6 M ammonium sulfate, 0.1 M HEPES, 0.1 M sodium chloride, 0.5 M NADH, 0.15 M FAD. anaerobic crystallization. 0.5 uM XiaP (protein, reductase)
Crystal Properties Matthews coefficient Solvent content 4.51 72.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.6 α = 90 b = 166.6 β = 90 c = 99.66 γ = 120
Symmetry Space Group P 62 2 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 PIXEL DECTRIS EIGER X 16M 2015-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.9 30 95.3 0.084 18.8 9.1 17733
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 2.9 3 96.9 0.525 5.9
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 2JBR 2.9 15 16846 887 95.42 0.17504 0.17359 0.179 0.20199 0.2076 RANDOM 65.091
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] 1.01 1.01 1.01 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.583 r_sphericity_free 32.509 r_dihedral_angle_4_deg 18.327 r_dihedral_angle_3_deg 16.881 r_sphericity_bonded 5.345 r_dihedral_angle_1_deg 4.171 r_long_range_B_refined 3.182 r_long_range_B_other 3.182 r_mcangle_it 2.496 r_mcangle_other 2.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.583 r_sphericity_free 32.509 r_dihedral_angle_4_deg 18.327 r_dihedral_angle_3_deg 16.881 r_sphericity_bonded 5.345 r_dihedral_angle_1_deg 4.171 r_long_range_B_refined 3.182 r_long_range_B_other 3.182 r_mcangle_it 2.496 r_mcangle_other 2.496 r_scangle_other 2.382 r_scbond_it 1.956 r_scbond_other 1.938 r_mcbond_it 1.919 r_mcbond_other 1.894 r_angle_refined_deg 0.846 r_angle_other_deg 0.69 r_rigid_bond_restr 0.639 r_chiral_restr 0.042 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2954 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing