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XiaF from Streptomyces sp. in complex with FADH2 and Glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.6 M (NH4)2SO4, 0.1 M HEPES, 0.1 M NaCl, 0.1 M NADH, 0.15 M FAD, 10% Glycerol, anaerobic crystallization 0.0005 mM XiaP (protein, reductase)
Crystal Properties Matthews coefficient Solvent content 4.59 73.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.93 α = 89.96 b = 167.09 β = 90.18 c = 200.94 γ = 119.82
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 PILATUS3 S 6M 2016-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 2.4 30 95.5 0.098 7.4 1.9 703582
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 2.4 2.5 94.8 0.578 2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5LVW 2.4 15 665721 35038 95.12 0.19975 0.19822 0.22881 0.1857 RANDOM 38.471
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] 0.66 0.62 -1.62 1.08 0.59 -3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.934 r_sphericity_free 31.566 r_dihedral_angle_4_deg 19.066 r_dihedral_angle_3_deg 17.192 r_sphericity_bonded 14.276 r_long_range_B_refined 5.126 r_long_range_B_other 4.98 r_scangle_other 4.369 r_dihedral_angle_1_deg 3.906 r_mcangle_it 3.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.934 r_sphericity_free 31.566 r_dihedral_angle_4_deg 19.066 r_dihedral_angle_3_deg 17.192 r_sphericity_bonded 14.276 r_long_range_B_refined 5.126 r_long_range_B_other 4.98 r_scangle_other 4.369 r_dihedral_angle_1_deg 3.906 r_mcangle_it 3.816 r_mcangle_other 3.816 r_scbond_it 3.559 r_scbond_other 3.558 r_rigid_bond_restr 2.931 r_mcbond_it 2.884 r_mcbond_other 2.881 r_angle_refined_deg 1.654 r_angle_other_deg 1.045 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 71448 Nucleic Acid Atoms Solvent Atoms 4679 Heterogen Atoms 1416
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing