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STRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JG2 PDB ENTRY 1JG2, MONOMER A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.53 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.548 α = 90 b = 96.38 β = 94.29 c = 94.841 γ = 90
Symmetry Space Group P 1 21 1
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 32.8 98.5 0.07 12.9 4.2 87737 26.9
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 2.11 98.5 0.48 3 4.3
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 1JG2, MONOMER A 2 38.2 92409 4672 98.3 0.201 0.198 0.1991 0.247 0.2449 RANDOM 32.02
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] 0.68 -1.08 -0.61 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.607 r_dihedral_angle_4_deg 23.097 r_dihedral_angle_3_deg 15.061 r_dihedral_angle_1_deg 5.587 r_scangle_it 2.658 r_mcangle_it 2.506 r_scbond_it 1.733 r_mcbond_it 1.626 r_angle_refined_deg 1.129 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.607 r_dihedral_angle_4_deg 23.097 r_dihedral_angle_3_deg 15.061 r_dihedral_angle_1_deg 5.587 r_scangle_it 2.658 r_mcangle_it 2.506 r_scbond_it 1.733 r_mcbond_it 1.626 r_angle_refined_deg 1.129 r_nbtor_refined 0.31 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_vdw_other 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 9619 Nucleic Acid Atoms Solvent Atoms 591 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing