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Crystal structure of a short chain dehydrogenase from Mycobacterium avium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZBQ PDB ENTRY 1ZBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 MymaA.01582.a.A1 PS00686 at 57.1 mg/mL against JCSG+ screen condition C11, 0.1 M NaOAc pH 4.6, 2 M ammonium sulfate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217306c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.52 α = 90 b = 129.9 β = 109.86 c = 91.86 γ = 90
Symmetry Space Group P 1 21 1
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 2011-01-23 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 1.8 50 99.8 0.052 18.1 4.6 166151 165849 -3
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 1.8 1.85 99.8 0.435 3.35 4.3
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZBQ 1.8 50 157404 8334 99.84 0.16164 0.15993 0.161 0.19405 0.1938 RANDOM 27.037
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] 0.59 0.48 -0.5 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.61 r_dihedral_angle_4_deg 16.174 r_dihedral_angle_3_deg 11.689 r_dihedral_angle_1_deg 5.647 r_scangle_it 3.475 r_scbond_it 2.174 r_angle_refined_deg 1.365 r_mcangle_it 1.276 r_mcbond_it 0.743 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.61 r_dihedral_angle_4_deg 16.174 r_dihedral_angle_3_deg 11.689 r_dihedral_angle_1_deg 5.647 r_scangle_it 3.475 r_scbond_it 2.174 r_angle_refined_deg 1.365 r_mcangle_it 1.276 r_mcbond_it 0.743 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12121 Nucleic Acid Atoms Solvent Atoms 1273 Heterogen Atoms 45
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction