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Crystal structure of N-Acetylmannosamine kinase in complex with N- acetyl mannosamine 6-phosphate and ADP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YHW PDB ENTRY 2YHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M CALCIUM ACETATE, 0.1M SODIUM CACODYLATE PH 6.5 AND 40% PEG 300
Crystal Properties Matthews coefficient Solvent content 2.85 56.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.7 α = 90 b = 90.7 β = 90 c = 101.49 γ = 90
Symmetry Space Group P 41 21 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 2.1 41.4 99.3 0.07 18.1 5.4 24925 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 2.1 2.16 96.2 0.69 2 3.9
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 2YHW 2.15 41.4 22395 1179 100 0.16791 0.16667 0.1729 0.19101 0.1922 RANDOM 37.126
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] 0.37 0.37 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 24.751 r_dihedral_angle_3_deg 15.252 r_dihedral_angle_1_deg 6.465 r_scangle_it 4.808 r_scbond_it 3.007 r_angle_refined_deg 1.788 r_mcangle_it 1.756 r_angle_other_deg 1.014 r_mcbond_it 0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 24.751 r_dihedral_angle_3_deg 15.252 r_dihedral_angle_1_deg 6.465 r_scangle_it 4.808 r_scbond_it 3.007 r_angle_refined_deg 1.788 r_mcangle_it 1.756 r_angle_other_deg 1.014 r_mcbond_it 0.976 r_mcbond_other 0.289 r_chiral_restr 0.108 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_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 2270 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing