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Crystal Structure of UDP-N-Acetylenolpyruvylglucosamine Reductase (MurB) from Thermus caldophilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100mM Mes-NaOH (pH 6.5), 18% (w/v) PEG 8000, 200mM CaCl2, 25mM substrate (EP-UDPGlcNAc), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.817 α = 65.26 b = 46.85 β = 76.13 c = 48.593 γ = 84.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 4 2005-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.000 PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 50 95.2 29519 29087
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.63 89.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.6 25.96 27619 27619 1467 95.13 0.17245 0.16972 0.1685 0.2232 0.2215 RANDOM 22.219
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 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.878 r_dihedral_angle_4_deg 15.125 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.788 r_sphericity_free 3.235 r_sphericity_bonded 2.874 r_scbond_it 2.594 r_rigid_bond_restr 1.98 r_mcangle_it 1.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.878 r_dihedral_angle_4_deg 15.125 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.788 r_sphericity_free 3.235 r_sphericity_bonded 2.874 r_scbond_it 2.594 r_rigid_bond_restr 1.98 r_mcangle_it 1.696 r_angle_refined_deg 1.401 r_mcbond_it 1.063 r_nbtor_refined 0.308 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.103 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2066 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling CNS phasing