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Crystal structure of alanine dehydrogenase/pyridine nucleotide transhydrogenase from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L7D PDB entry 1L7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 21.6 mg/mL MysmA.00681.a.A1 PS00596 against PACT screen condition C11 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2 M CaCl2, cryo-protected with 25% ethylene glycol, crystal tracking ID 215904c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.76 α = 90 b = 89.76 β = 90 c = 179.57 γ = 120
Symmetry Space Group P 61 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 QUANTUM 315r 2010-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
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 1.82 50 97.8 0.052 42.32 17.3 38305 -3 23.517
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 1.82 1.87 81.2 0.234 11.1 14.1 2842
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1L7D 1.82 40.15 38192 1913 97.56 0.1665 0.165 0.1963 0.1916 RANDOM 19.0145
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] -0.37 -0.18 -0.37 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.044 r_dihedral_angle_4_deg 22.038 r_dihedral_angle_3_deg 11.042 r_dihedral_angle_1_deg 5.184 r_scangle_it 4.225 r_scbond_it 2.414 r_mcangle_it 1.509 r_angle_refined_deg 1.428 r_mcbond_it 0.845 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.044 r_dihedral_angle_4_deg 22.038 r_dihedral_angle_3_deg 11.042 r_dihedral_angle_1_deg 5.184 r_scangle_it 4.225 r_scbond_it 2.414 r_mcangle_it 1.509 r_angle_refined_deg 1.428 r_mcbond_it 0.845 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2462 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction