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Crystal structure of thermostable variant of phosphite dehydrogenase from Pseudomonas stutzeri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 Sodium Chloride, MES, PEG4000
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.789 α = 90 b = 93.789 β = 90 c = 139.512 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 PIXEL DECTRIS EIGER2 X 9M 2024-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97857 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.83 50 99.6 0.307 0.314 0.064 1 14.3 21 27744
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 95.9 2.03 2.101 0.508 0.501 1.12 11.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.93 50 26272 1426 99.08 0.17269 0.17046 0.1808 0.21574 0.2246 RANDOM 27.434
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 0.3 0.59 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.474 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 12.715 r_dihedral_angle_1_deg 5.752 r_long_range_B_refined 5.537 r_long_range_B_other 5.236 r_scangle_other 2.659 r_mcangle_it 1.804 r_mcangle_other 1.803 r_scbond_it 1.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.474 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 12.715 r_dihedral_angle_1_deg 5.752 r_long_range_B_refined 5.537 r_long_range_B_other 5.236 r_scangle_other 2.659 r_mcangle_it 1.804 r_mcangle_other 1.803 r_scbond_it 1.626 r_scbond_other 1.613 r_angle_refined_deg 1.356 r_mcbond_it 1.12 r_mcbond_other 1.12 r_angle_other_deg 0.8 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2521 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing