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Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-Man
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350 -- 0.2M ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.38 48.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.08 α = 90 b = 114.438 β = 90 c = 140.536 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 2017-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96860 Diamond I24
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 1.94 63.91 100 5.8 6.5 110446
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 1.94 1.99 100 1.2 6.5
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 FOURIER SYNTHESIS THROUGHOUT 1T2A 1.94 63.9 104361 5308 99.26 0.21104 0.20967 0.2174 0.23847 0.2461 RANDOM 27.493
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] -0.81 1.82 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.702 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_1_deg 6.037 r_long_range_B_refined 4.693 r_long_range_B_other 4.683 r_scangle_other 3.304 r_mcangle_it 2.559 r_mcangle_other 2.559 r_scbond_it 2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.702 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_1_deg 6.037 r_long_range_B_refined 4.693 r_long_range_B_other 4.683 r_scangle_other 3.304 r_mcangle_it 2.559 r_mcangle_other 2.559 r_scbond_it 2.117 r_scbond_other 2.113 r_mcbond_it 1.71 r_mcbond_other 1.709 r_angle_refined_deg 1.482 r_angle_other_deg 0.944 r_chiral_restr 0.083 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 10832 Nucleic Acid Atoms Solvent Atoms 736 Heterogen Atoms 382
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing