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Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and Zn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EE2 PDB entry 1EE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 25% PEG 3350, 0.2 M Ammonium acetate, 0.1 M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.77 55.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.299 α = 90 b = 160.919 β = 111.64 c = 88.739 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 MARMOSAIC 225 mm CCD 2008-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9919 SLS X10SA
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 2.1 50 96 0.089 7.2 2.9 97589 97589 23
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 2.1 2.21 89 0.42 2 2.2 13182
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1EE2 2.1 49.39 95873 95873 1674 95.65 0.16958 0.16958 0.16893 0.172 0.20626 0.2058 RANDOM 19.963
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] 0.08 0.15 0.72 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.764 r_dihedral_angle_3_deg 13.099 r_dihedral_angle_4_deg 8.141 r_dihedral_angle_1_deg 5.668 r_scangle_it 4.842 r_scbond_it 3.788 r_mcangle_it 2 r_mcbond_it 1.463 r_angle_refined_deg 1.21 r_angle_other_deg 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.764 r_dihedral_angle_3_deg 13.099 r_dihedral_angle_4_deg 8.141 r_dihedral_angle_1_deg 5.668 r_scangle_it 4.842 r_scbond_it 3.788 r_mcangle_it 2 r_mcbond_it 1.463 r_angle_refined_deg 1.21 r_angle_other_deg 0.905 r_mcbond_other 0.242 r_symmetry_hbond_refined 0.229 r_nbd_other 0.18 r_nbd_refined 0.179 r_nbtor_refined 0.166 r_symmetry_vdw_other 0.14 r_xyhbond_nbd_refined 0.13 r_symmetry_vdw_refined 0.118 r_nbtor_other 0.081 r_chiral_restr 0.068 r_metal_ion_refined 0.015 r_bond_refined_d 0.01 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11167 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing