1H50

Structure of Pentaerythritol Tetranitrate Reductase and complexes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OYAPDB ENTRY 1OYA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.225% PEG 3000, 0.1M SODIUM ACETATE, 0.1M SODIUM CACODYLATE, 17% ISOPROPANOL PH 6.2
Crystal Properties
Matthews coefficientSolvent content
2.338

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.501α = 90
b = 68.492β = 90
c = 88.272γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV IMAGE PLATEMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.55091.70.04530.13.15101615.9
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)
11.50.12

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1OYA1.55050462244890.60.1930.1930.225RANDOM15.5
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]
-1.712.94-1.24
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.4
c_angle_deg1.3
c_improper_angle_d0.87
c_scangle_it0.85
c_mcangle_it0.68
c_scbond_it0.54
c_mcbond_it0.38
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.4
c_angle_deg1.3
c_improper_angle_d0.87
c_scangle_it0.85
c_mcangle_it0.68
c_scbond_it0.54
c_mcbond_it0.38
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2779
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms35

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
ARP/wARPphasing
CNSrefinement