5LGX

Structure of Oxidised Pentaerythritol Tetranitrate Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H50 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29825 % PEG 3000, 0.1 M sodium citrate, 0.1 M cacodylate pH 6.2, 17 % isopropanol
Crystal Properties
Matthews coefficientSolvent content
2.1943.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.76α = 90
b = 68.587β = 90
c = 88.574γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4920.8294.30.1310.14.753305
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.520.44

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1H501.520.8250507271593.990.158110.155840.20016RANDOM10.637
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]
-0.270.29-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.563
r_dihedral_angle_4_deg15.734
r_dihedral_angle_3_deg14.033
r_dihedral_angle_1_deg6.683
r_long_range_B_refined5.584
r_long_range_B_other5.584
r_scangle_other2.484
r_angle_refined_deg2.082
r_scbond_it1.631
r_scbond_other1.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.563
r_dihedral_angle_4_deg15.734
r_dihedral_angle_3_deg14.033
r_dihedral_angle_1_deg6.683
r_long_range_B_refined5.584
r_long_range_B_other5.584
r_scangle_other2.484
r_angle_refined_deg2.082
r_scbond_it1.631
r_scbond_other1.631
r_mcangle_it1.599
r_mcangle_other1.598
r_angle_other_deg1.123
r_mcbond_it1.052
r_mcbond_other1.046
r_chiral_restr0.133
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms2769
Nucleic Acid Atoms
Solvent Atoms618
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing