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Crystal structure of pseudomonas aeruginosa 1,6-anhydro-n-actetylmuramic acid kinase (ANMK) bound to adenosine diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 296 25% PEG 4000, 0.2 M (NH4)2SO4, 0.1 M tri-Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.56 51.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.218 α = 90 b = 90.218 β = 90 c = 174.82 γ = 120
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 RAYONIX MX-300 2010-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.23 46.71 100 0.082 0.087 16.7 8.6 56308 39204 3 36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.23 2.35 99.8 0.397 0.43 4.6 6.8 5683
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 (All) 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 3CQY 2.23 46.71 39204 37465 1691 99.78 0.18884 0.18884 0.18783 0.2153 0.21034 0.2331 RANDOM 35.154
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] -10.95 -10.95 21.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.586 r_dihedral_angle_4_deg 17.296 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 5.374 r_scangle_it 2.529 r_scbond_it 1.531 r_angle_refined_deg 1.173 r_mcangle_it 0.969 r_mcbond_it 0.514 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.586 r_dihedral_angle_4_deg 17.296 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 5.374 r_scangle_it 2.529 r_scbond_it 1.531 r_angle_refined_deg 1.173 r_mcangle_it 0.969 r_mcbond_it 0.514 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5228 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 64
Software Software Software Name Purpose MxDC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling