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The X-ray crystal structure of DesE bound to desferrioxamine B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X4L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 2.63M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.24M NACL.
Crystal Properties Matthews coefficient Solvent content 2.26 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.163 α = 90 b = 58.055 β = 90 c = 101.194 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 RIGAKU 2009-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.96 30.99 94.3 0.059 19.8 5.8 20684
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 1.96 2.01 95.5 0.12 10.3 5.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2x4l 1.96 30.99 20684 1123 94.24 0.16172 0.15947 0.1717 0.20423 0.2126 RANDOM 19.665
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 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.214 r_dihedral_angle_4_deg 21.571 r_dihedral_angle_3_deg 12.729 r_dihedral_angle_1_deg 6.045 r_long_range_B_other 4.329 r_long_range_B_refined 4.327 r_scangle_other 2.506 r_scbond_it 1.589 r_scbond_other 1.589 r_angle_refined_deg 1.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.214 r_dihedral_angle_4_deg 21.571 r_dihedral_angle_3_deg 12.729 r_dihedral_angle_1_deg 6.045 r_long_range_B_other 4.329 r_long_range_B_refined 4.327 r_scangle_other 2.506 r_scbond_it 1.589 r_scbond_other 1.589 r_angle_refined_deg 1.499 r_mcangle_it 1.421 r_mcangle_other 1.42 r_mcbond_it 0.943 r_mcbond_other 0.941 r_angle_other_deg 0.914 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 2267 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing