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Thermostable phosphite dehydrogenase in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EBF Thermostable phosphite dehydrogenase E175A variant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 285 25-30% PEG 3350, 100 mM KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.29 46.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.71 α = 90 b = 113.54 β = 100.16 c = 130.19 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 1.7 80 95 0.054 19.2 6 270433
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 1.7 1.8 74.1 0.436 3 3.8 44707
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 Thermostable phosphite dehydrogenase E175A variant 1.7 25 256745 13623 100 0.212 0.21016 0.24698 0.2477 RANDOM 29.973
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] 0.44 -0.23 -1.33 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.545 r_dihedral_angle_4_deg 15.603 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.371 r_scangle_it 2.293 r_scbond_it 1.374 r_angle_refined_deg 1.159 r_mcangle_it 0.918 r_mcbond_it 0.481 r_angle_other_deg 0.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.545 r_dihedral_angle_4_deg 15.603 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.371 r_scangle_it 2.293 r_scbond_it 1.374 r_angle_refined_deg 1.159 r_mcangle_it 0.918 r_mcbond_it 0.481 r_angle_other_deg 0.252 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 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 20133 Nucleic Acid Atoms Solvent Atoms 2458 Heterogen Atoms 352
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling