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X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S4N PDB ENTRY 1S4N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M NA-CACODYLATE, PH 6.5 0.2M CAOAC 18% (W/V) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.198 α = 90 b = 102.368 β = 90 c = 156.908 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 PIXEL KB MIRROR 2014-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.2 50 99.7 0.13 13.8 7.8 49674 2
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 2.2 2.28 97 0.65 3 8
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 PDB ENTRY 1S4N 2.21 85.74 47109 2420 99.7 0.16502 0.16311 0.1715 0.20273 0.2066 RANDOM 24.972
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.921 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 6.436 r_scangle_it 4.82 r_scbond_it 3.12 r_mcangle_it 3.082 r_mcbond_it 2.111 r_mcbond_other 2.111 r_angle_refined_deg 1.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.921 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 6.436 r_scangle_it 4.82 r_scbond_it 3.12 r_mcangle_it 3.082 r_mcbond_it 2.111 r_mcbond_other 2.111 r_angle_refined_deg 1.684 r_angle_other_deg 1.122 r_metal_ion_refined 0.461 r_symmetry_metal_ion_refined 0.446 r_symmetry_vdw_refined 0.393 r_nbd_refined 0.277 r_nbtor_refined 0.202 r_symmetry_vdw_other 0.196 r_nbd_other 0.195 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.102 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.08 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.006 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6538 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing