3P62

Wild-type pentaerythritol tetranitrate reductase containing a C-terminal 8-histidine tag


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H50PDB ENTRY 1H50

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.2293100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.961α = 90
b = 68.954β = 90
c = 88.476γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 12009-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.07ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.454.39399.50.0670.06712.73.47125271252
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4899.90.290.290.3450.1842.53.410357

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 1H501.427.9771195360599.340.12730.12580.1559RANDOM14.9066
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.298
r_dihedral_angle_4_deg16.168
r_dihedral_angle_3_deg12.111
r_sphericity_free5.991
r_dihedral_angle_1_deg5.738
r_scangle_it3.293
r_sphericity_bonded2.698
r_scbond_it2.457
r_mcangle_it1.678
r_angle_refined_deg1.436
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.298
r_dihedral_angle_4_deg16.168
r_dihedral_angle_3_deg12.111
r_sphericity_free5.991
r_dihedral_angle_1_deg5.738
r_scangle_it3.293
r_sphericity_bonded2.698
r_scbond_it2.457
r_mcangle_it1.678
r_angle_refined_deg1.436
r_mcbond_it1.303
r_rigid_bond_restr1.209
r_angle_other_deg0.949
r_mcbond_other0.578
r_symmetry_vdw_other0.318
r_symmetry_hbond_refined0.248
r_nbd_other0.218
r_nbd_refined0.217
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.148
r_symmetry_vdw_refined0.106
r_chiral_restr0.086
r_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2776
Nucleic Acid Atoms
Solvent Atoms698
Heterogen Atoms35

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction