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Crystal structure of PA4631, a nucleoside-diphosphate-sugar epimerase from Pseudomonas aeruginosa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 2.55M NACL, 0.1M HEPES PH 8 OR 2.9M NACL, 0.1M BICINE PH 8.5 AT A PROTEIN CONCENTRATION OF 2 MG ML-1.CRYSTALS WERE CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 18% GLYCEROL. CRYSTAL WAS SOAKED IN 20MM TRIMETHYLLEADCHLORIDE FOR APPROXIMATELY 5 MINUTES BEFORE BEING BACK SOAKED IN CRYO BUFFER
Crystal Properties Matthews coefficient Solvent content 2.91 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.38 α = 90 b = 83.38 β = 90 c = 215.72 γ = 120
Symmetry Space Group P 62 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 ADSC CCD MIRRORS 2008-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.65 41.7 97 0.08 23.3 5 12600
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 2.65 2.7 90 0.66 2.75 3.4
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NONE 2.65 41.7 12600 679 97 0.21346 0.21142 0.2141 0.25314 0.2479 RANDOM 30.888
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] 0.92 0.46 0.92 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.401 r_dihedral_angle_4_deg 18.631 r_dihedral_angle_3_deg 16.635 r_dihedral_angle_1_deg 6.319 r_scangle_it 2.945 r_scbond_it 1.691 r_angle_refined_deg 1.332 r_mcangle_it 1.111 r_angle_other_deg 0.845 r_mcbond_it 0.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.401 r_dihedral_angle_4_deg 18.631 r_dihedral_angle_3_deg 16.635 r_dihedral_angle_1_deg 6.319 r_scangle_it 2.945 r_scbond_it 1.691 r_angle_refined_deg 1.332 r_mcangle_it 1.111 r_angle_other_deg 0.845 r_mcbond_it 0.564 r_mcbond_other 0.078 r_chiral_restr 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 2301 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling SHELXCDE phasing