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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 8.5 289 Magnesium chloride, TRIS, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.46 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.711 α = 90 b = 93.711 β = 90 c = 140.657 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 2024-04-02 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 1.82 82.34 100 0.406 0.416 0.091 0.995 17.1 20.3 33281
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 4.94 50 100 0.057 0.059 0.013 1 20.9
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 1.82 46.93 31659 1572 99.94 0.15864 0.15702 0.169 0.19131 0.2009 RANDOM 21.433
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] 0.38 0.19 0.38 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.354 r_dihedral_angle_1_deg 6.448 r_long_range_B_refined 5.526 r_long_range_B_other 5.167 r_dihedral_angle_2_deg 5.153 r_scangle_other 3.422 r_scbond_it 2.052 r_scbond_other 2.051 r_mcangle_other 1.903 r_mcangle_it 1.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.354 r_dihedral_angle_1_deg 6.448 r_long_range_B_refined 5.526 r_long_range_B_other 5.167 r_dihedral_angle_2_deg 5.153 r_scangle_other 3.422 r_scbond_it 2.052 r_scbond_other 2.051 r_mcangle_other 1.903 r_mcangle_it 1.902 r_angle_refined_deg 1.323 r_mcbond_it 1.224 r_mcbond_other 1.224 r_angle_other_deg 0.479 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2522 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing