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Crystal structure of holo L-alanine dehydrogenase from Mycobacterium tuberculosis in the closed conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8
Crystal Properties Matthews coefficient Solvent content 2.76 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.991 α = 90 b = 140.991 β = 90 c = 140.991 γ = 90
Symmetry Space Group P 21 3
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 SINGLE SILICON 2007-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.04 47.7 100 0.1 10.1 6 359770 2.8
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 2.04 2.15 100 0.58 2.8 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.04 40 56464 2984 99.9 0.166 0.164 0.204 0.2079 RANDOM 40.07
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 16.152 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_1_deg 5.716 r_scangle_it 3.263 r_scbond_it 2.139 r_angle_refined_deg 1.464 r_mcangle_it 1.166 r_mcbond_it 0.747 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 16.152 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_1_deg 5.716 r_scangle_it 3.263 r_scbond_it 2.139 r_angle_refined_deg 1.464 r_mcangle_it 1.166 r_mcbond_it 0.747 r_nbtor_refined 0.302 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.144 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.099 r_bond_refined_d 0.013 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 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 5438 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing