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Xanthomonas campestris putative OGT (XCC0866), complex with UDP- GlcNAc phosphonate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VSY PDB ENTRY 2VSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 83 MM CHES PH 9.0, 20.8% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.86 α = 90 b = 100.527 β = 90 c = 154.521 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 CCD ADSC CCD 2008-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.5 20 95.1 0.1 10.2 4.3 43895
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 2.5 2.59 92.5 0.39 2.73 4
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VSY 2.5 19.83 42804 903 95.4 0.211 0.21 0.2111 0.247 RANDOM 27.78
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 0.06 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_3_deg 17.029 r_dihedral_angle_4_deg 16.312 r_dihedral_angle_1_deg 7.308 r_scangle_it 2.61 r_scbond_it 1.53 r_angle_refined_deg 1.464 r_mcangle_it 0.944 r_mcbond_it 0.476 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_3_deg 17.029 r_dihedral_angle_4_deg 16.312 r_dihedral_angle_1_deg 7.308 r_scangle_it 2.61 r_scbond_it 1.53 r_angle_refined_deg 1.464 r_mcangle_it 0.944 r_mcbond_it 0.476 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 8342 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling