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Crystal structure of fucosyltransferase NodZ from Bradyrhizobium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.25M potassium dihydrogen phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.83 56.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.2 α = 90 b = 124.2 β = 90 c = 96.1 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2004-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8128 EMBL/DESY, HAMBURG X11
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 1.54 15 100 0.05 72.5 24.4 64545 -3 26.31
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 1.54 1.57 100 0.802 3.8 17.8 3171
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.54 15 62474 62469 1270 96.8 0.183 0.182 0.1924 0.197 0.2015 RANDOM 29.03
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] -1.04 -0.52 -1.04 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.293 r_dihedral_angle_4_deg 20.705 r_dihedral_angle_3_deg 12.95 r_dihedral_angle_1_deg 5.523 r_scangle_it 3.786 r_scbond_it 2.672 r_angle_refined_deg 1.705 r_mcangle_it 1.508 r_mcbond_it 1.284 r_mcbond_other 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.293 r_dihedral_angle_4_deg 20.705 r_dihedral_angle_3_deg 12.95 r_dihedral_angle_1_deg 5.523 r_scangle_it 3.786 r_scbond_it 2.672 r_angle_refined_deg 1.705 r_mcangle_it 1.508 r_mcbond_it 1.284 r_mcbond_other 0.321 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.215 r_nbd_other 0.205 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.186 r_symmetry_vdw_other 0.16 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.1 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2341 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing