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Crystal structure of Anabaena Alr3699/HepE in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 1.0M ammonium citrate tribasic pH 7.0, 0.1M Bis-Tris propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.22 44.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.883 α = 90 b = 133.223 β = 90 c = 143.019 γ = 90
Symmetry Space Group C 2 2 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 315r 2014-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97923 SSRF BL17U
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 2.15 50 99.5 0.085 19.16 4 41058
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 2.15 2.23 99.8 0.501 3.48 4
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 4XSO 2.15 35.78 38849 2054 99.01 0.20776 0.20584 0.2083 0.24371 0.2468 RANDOM 42.134
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] 2.26 -1.34 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.162 r_dihedral_angle_4_deg 19.192 r_dihedral_angle_3_deg 13.248 r_long_range_B_other 6.802 r_long_range_B_refined 6.795 r_dihedral_angle_1_deg 5.548 r_scangle_other 5.282 r_mcangle_it 3.847 r_mcangle_other 3.847 r_scbond_it 3.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.162 r_dihedral_angle_4_deg 19.192 r_dihedral_angle_3_deg 13.248 r_long_range_B_other 6.802 r_long_range_B_refined 6.795 r_dihedral_angle_1_deg 5.548 r_scangle_other 5.282 r_mcangle_it 3.847 r_mcangle_other 3.847 r_scbond_it 3.413 r_scbond_other 3.412 r_mcbond_it 2.695 r_mcbond_other 2.691 r_angle_refined_deg 1.334 r_angle_other_deg 0.757 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 5570 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP model building HKL-2000 data reduction iMOSFLM phasing