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Crystal structure of fucosyltransferase NodZ from Bradyrhizobium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HHC PDB ENTRY 2HHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 0.25M potassium dihydrogen phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.1 α = 90 b = 130.1 β = 90 c = 83.3 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 BW7A EMBL/DESY, HAMBURG BW7A
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 1.95 15 99.9 0.045 58.2 11.7 30716 -3 24.2
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 1.95 2.01 100 0.27 11.9 11.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2HHC 1.95 15 30716 30711 1085 99.9 0.162 0.161 0.1742 0.206 0.212 RANDOM 27.03
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] -0.13 -0.06 -0.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.644 r_dihedral_angle_4_deg 16.907 r_dihedral_angle_3_deg 12.597 r_dihedral_angle_1_deg 5.975 r_scangle_it 5.287 r_scbond_it 3.929 r_mcangle_it 1.704 r_angle_refined_deg 1.599 r_mcbond_it 1.339 r_symmetry_vdw_other 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.644 r_dihedral_angle_4_deg 16.907 r_dihedral_angle_3_deg 12.597 r_dihedral_angle_1_deg 5.975 r_scangle_it 5.287 r_scbond_it 3.929 r_mcangle_it 1.704 r_angle_refined_deg 1.599 r_mcbond_it 1.339 r_symmetry_vdw_other 0.285 r_symmetry_vdw_refined 0.262 r_mcbond_other 0.255 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.198 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.091 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_nbd_other r_nbtor_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 2301 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling MOLREP phasing