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Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-Man
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350, 0.15M DL- malic acid
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.73 α = 90 b = 114.532 β = 90 c = 140.061 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 PIXEL DECTRIS PILATUS 6M 2017-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.47 140.06 100 17.2 6.7 254599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.55 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.47 88.66 241686 12794 99.96 0.14226 0.14056 0.17434 0.1814 RANDOM 23.674
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] -0.82 1.9 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.574 r_sphericity_free 27.232 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_3_deg 12.157 r_sphericity_bonded 11.465 r_dihedral_angle_1_deg 6.119 r_long_range_B_refined 3.642 r_long_range_B_other 3.642 r_scangle_other 2.683 r_mcangle_it 2.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.574 r_sphericity_free 27.232 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_3_deg 12.157 r_sphericity_bonded 11.465 r_dihedral_angle_1_deg 6.119 r_long_range_B_refined 3.642 r_long_range_B_other 3.642 r_scangle_other 2.683 r_mcangle_it 2.379 r_mcangle_other 2.379 r_scbond_it 2.12 r_scbond_other 2.12 r_rigid_bond_restr 1.817 r_mcbond_it 1.814 r_mcbond_other 1.812 r_angle_refined_deg 1.505 r_angle_other_deg 0.975 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10903 Nucleic Acid Atoms Solvent Atoms 858 Heterogen Atoms 466
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing