3P8I

Y351F mutant of pentaerythritol tetranitrate reductase containing a bound acetate molecule


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
2.1943.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.685α = 90
b = 68.838β = 90
c = 88.915γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 12008-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.970ESRFID14-4

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
11.1937.499.30.07710.63.8111179111179
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)
1.191.2399.70.2484.4

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 REPLACEMENTTHROUGHOUT1H501.197.98110924556499.50.13020.12930.1467RANDOM13.1949
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.523
r_dihedral_angle_4_deg15.308
r_dihedral_angle_3_deg11.936
r_dihedral_angle_1_deg5.67
r_sphericity_free4.571
r_sphericity_bonded3.488
r_scangle_it3.012
r_scbond_it2.118
r_mcangle_it1.545
r_angle_refined_deg1.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.523
r_dihedral_angle_4_deg15.308
r_dihedral_angle_3_deg11.936
r_dihedral_angle_1_deg5.67
r_sphericity_free4.571
r_sphericity_bonded3.488
r_scangle_it3.012
r_scbond_it2.118
r_mcangle_it1.545
r_angle_refined_deg1.381
r_angle_other_deg1.379
r_mcbond_it1.202
r_rigid_bond_restr1.095
r_mcbond_other0.867
r_symmetry_vdw_other0.294
r_symmetry_hbond_refined0.261
r_symmetry_vdw_refined0.244
r_nbd_other0.224
r_nbd_refined0.211
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.128
r_chiral_restr0.082
r_nbtor_other0.077
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2758
Nucleic Acid Atoms
Solvent Atoms774
Heterogen Atoms35

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
d*TREKdata reduction