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XiaF (apo) 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
Crystal Properties Matthews coefficient Solvent content 4.48 72.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.54 α = 90 b = 166.54 β = 90 c = 98.97 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 2.6 30 99.6 0.085 16.5 10.9 25318
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 2.6 2.7 99.7 0.563 4.3
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 2.6 15 24035 1265 99.65 0.18398 0.18223 0.1852 0.21759 0.2125 RANDOM 64.744
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] 0.9 0.9 0.9 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.319 r_sphericity_free 23.471 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 15.468 r_sphericity_bonded 11.443 r_dihedral_angle_1_deg 4.131 r_long_range_B_refined 3.554 r_long_range_B_other 3.381 r_mcangle_it 3 r_mcangle_other 3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.319 r_sphericity_free 23.471 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 15.468 r_sphericity_bonded 11.443 r_dihedral_angle_1_deg 4.131 r_long_range_B_refined 3.554 r_long_range_B_other 3.381 r_mcangle_it 3 r_mcangle_other 3 r_scangle_other 2.744 r_mcbond_it 2.27 r_scbond_it 2.264 r_scbond_other 2.256 r_mcbond_other 2.233 r_angle_refined_deg 0.788 r_angle_other_deg 0.689 r_rigid_bond_restr 0.554 r_chiral_restr 0.04 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 62 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing