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Thermostable phosphite dehydrogenase in complex with NAD and sulfite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EBF 12X Phosphite dehydrogenase E175A mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 285 25-30% PEG 3350, 100 mM KCl, 5 mM NAD, 5 mM sulfite, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.06 α = 90 b = 114.18 β = 112.33 c = 88.31 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 CCD MARMOSAIC 300 mm CCD 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 1.95 82 97.8 0.068 16.27 4.6 95305
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 1.95 2 84.9 0.41 3.2 3.5
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 12X Phosphite dehydrogenase E175A mutant 1.95 25 90507 4764 100 0.22141 0.21903 0.26677 0.2795 RANDOM 38.685
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] -0.58 -1.71 -2.02 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.592 r_dihedral_angle_3_deg 16.419 r_dihedral_angle_4_deg 16.236 r_dihedral_angle_1_deg 5.938 r_scangle_it 2.244 r_scbond_it 1.5 r_angle_refined_deg 1.453 r_mcangle_it 0.847 r_mcbond_it 0.506 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.592 r_dihedral_angle_3_deg 16.419 r_dihedral_angle_4_deg 16.236 r_dihedral_angle_1_deg 5.938 r_scangle_it 2.244 r_scbond_it 1.5 r_angle_refined_deg 1.453 r_mcangle_it 0.847 r_mcbond_it 0.506 r_chiral_restr 0.091 r_bond_refined_d 0.012 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 10068 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 192
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling