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L-arabinitol 4-dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PL7 PDB entry 1PL7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 278 1.8M ammonium sulfate
10 mM NAD
100 mM KCl
10 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.74 67.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.52 α = 90 b = 134.52 β = 90 c = 224.34 γ = 120
Symmetry Space Group P 64 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 IMAGE PLATE MAR scanner 300 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 2.6 50 96.3 0.094 13.3 10.6 34261
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) 2.6 2.69 92 0.632 2.9 8.6 3180
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 1PL7 2.6 25 33999 1793 100 0.21145 0.20863 0.2077 0.26634 0.2629 RANDOM 60.294
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] 0.1 0.05 0.1 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.815 r_dihedral_angle_3_deg 20.51 r_dihedral_angle_4_deg 20.412 r_dihedral_angle_1_deg 6.675 r_scangle_it 2.916 r_scbond_it 1.665 r_angle_refined_deg 1.562 r_mcangle_it 1.246 r_mcbond_it 0.657 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.815 r_dihedral_angle_3_deg 20.51 r_dihedral_angle_4_deg 20.412 r_dihedral_angle_1_deg 6.675 r_scangle_it 2.916 r_scbond_it 1.665 r_angle_refined_deg 1.562 r_mcangle_it 1.246 r_mcbond_it 0.657 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 5416 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 92
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling