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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, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.01 38.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.717 α = 64.83 b = 46.501 β = 77.04 c = 48.714 γ = 84.4
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 2005-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.15 50 93.6 77981 76514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.15 1.17 90.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.3 23.07 51088 51088 2740 95.13 0.18851 0.18736 0.2092 0.2086 RANDOM 18.297
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] 0.04 -0.02 0.06 -0.09 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.256 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 13.205 r_dihedral_angle_1_deg 5.952 r_sphericity_bonded 2.806 r_sphericity_free 2.801 r_scangle_it 2.645 r_scbond_it 1.847 r_mcangle_it 1.394 r_angle_refined_deg 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.256 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 13.205 r_dihedral_angle_1_deg 5.952 r_sphericity_bonded 2.806 r_sphericity_free 2.801 r_scangle_it 2.645 r_scbond_it 1.847 r_mcangle_it 1.394 r_angle_refined_deg 1.2 r_rigid_bond_restr 1.09 r_mcbond_it 0.875 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.075 r_metal_ion_refined 0.063 r_bond_refined_d 0.007 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_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 2075 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling CNS phasing