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Crystal Structure of Core-mannan synthase A (CmsA/Ktr4) from Aspergillus fumigatus, Mn/GDP-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.77 67.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.504 α = 90 b = 273.006 β = 90 c = 186.279 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 PIXEL DECTRIS EIGER X 16M 2019-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.9 44.82 99.89 0.066 0.072 0.999 15.36 6.9 306207
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968 0.734 0.792 0.8 1.91
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 5A07 1.9 44.82 291096 15120 99.89 0.16132 0.16029 0.1678 0.1812 0.1872 RANDOM 39.783
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] 1.28 -1.86 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 14.493 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_1_deg 6.218 r_long_range_B_refined 5.636 r_long_range_B_other 5.306 r_scangle_other 3.441 r_mcangle_it 2.443 r_mcangle_other 2.443 r_scbond_it 2.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 14.493 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_1_deg 6.218 r_long_range_B_refined 5.636 r_long_range_B_other 5.306 r_scangle_other 3.441 r_mcangle_it 2.443 r_mcangle_other 2.443 r_scbond_it 2.156 r_scbond_other 2.156 r_mcbond_it 1.632 r_mcbond_other 1.632 r_angle_refined_deg 1.304 r_angle_other_deg 0.906 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 18408 Nucleic Acid Atoms Solvent Atoms 1980 Heterogen Atoms 295
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing