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X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A08 PDB ENTRY 5A08
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 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.215 α = 90 b = 102.621 β = 90 c = 162.651 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 TOROIDAL MIRROR 2014-06-18 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 1.9 50 99.1 0.1 15.5 9.8 81509 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 1.9 1.94 98.9 0.87 2.3 9.2
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 5A08 1.9 86.79 76662 3941 98.89 0.15798 0.15627 0.1691 0.19132 0.2014 RANDOM 26.426
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] 2.59 -1.67 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 19.235 r_dihedral_angle_3_deg 13.76 r_dihedral_angle_1_deg 6.294 r_scangle_it 5.823 r_scbond_it 3.818 r_mcangle_it 3.111 r_mcbond_it 2.386 r_mcbond_other 2.385 r_angle_refined_deg 1.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 19.235 r_dihedral_angle_3_deg 13.76 r_dihedral_angle_1_deg 6.294 r_scangle_it 5.823 r_scbond_it 3.818 r_mcangle_it 3.111 r_mcbond_it 2.386 r_mcbond_other 2.385 r_angle_refined_deg 1.828 r_angle_other_deg 1.258 r_symmetry_vdw_refined 0.388 r_nbd_refined 0.276 r_nbtor_refined 0.196 r_nbd_other 0.189 r_symmetry_vdw_other 0.183 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.118 r_nbtor_other 0.086 r_xyhbond_nbd_other 0.037 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.005 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 6606 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing