8V36

Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with NADH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293HEPES, magnesium chloride, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.4249.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.307α = 90
b = 87.556β = 90
c = 134.197γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.23544.7399.70.0490.022112.76.744738
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.242.311.1390.5120.7521.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.23543.89644674226199.6390.2260.22260.280571.98
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]
5.424-1.048-4.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg13.707
r_dihedral_angle_3_deg13.322
r_lrange_it8.967
r_lrange_other8.967
r_mcangle_it6.15
r_mcangle_other6.149
r_dihedral_angle_1_deg6.132
r_scangle_it5.891
r_scangle_other5.89
r_dihedral_angle_2_deg5.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg13.707
r_dihedral_angle_3_deg13.322
r_lrange_it8.967
r_lrange_other8.967
r_mcangle_it6.15
r_mcangle_other6.149
r_dihedral_angle_1_deg6.132
r_scangle_it5.891
r_scangle_other5.89
r_dihedral_angle_2_deg5.439
r_mcbond_it3.802
r_mcbond_other3.802
r_scbond_it3.544
r_scbond_other3.543
r_angle_refined_deg0.92
r_angle_other_deg0.315
r_nbd_other0.222
r_nbd_refined0.205
r_symmetry_nbd_other0.184
r_nbtor_refined0.174
r_symmetry_xyhbond_nbd_other0.169
r_xyhbond_nbd_refined0.161
r_symmetry_xyhbond_nbd_refined0.097
r_symmetry_nbd_refined0.091
r_symmetry_nbtor_other0.076
r_metal_ion_refined0.064
r_dihedral_angle_other_2_deg0.05
r_chiral_restr0.042
r_chiral_restr_other0.007
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6268
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing