3P67

T26S mutant of pentaerythritol tetranitrate reductase containing a bound acetate molecule


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
2.1542.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.919α = 90
b = 69.063β = 90
c = 88.871γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.542

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
11.554.55499.80.0540.05419.64.55670556705
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)
1.51.581000.1640.1640.1880.0894.34.38161

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 1H501.516.3556644287299.870.1470.14580.1706RANDOM14.5332
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.756
r_dihedral_angle_4_deg15.243
r_dihedral_angle_3_deg12.626
r_dihedral_angle_1_deg5.471
r_sphericity_free3.262
r_scangle_it2.238
r_scbond_it1.658
r_sphericity_bonded1.385
r_angle_refined_deg1.212
r_mcangle_it1.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.756
r_dihedral_angle_4_deg15.243
r_dihedral_angle_3_deg12.626
r_dihedral_angle_1_deg5.471
r_sphericity_free3.262
r_scangle_it2.238
r_scbond_it1.658
r_sphericity_bonded1.385
r_angle_refined_deg1.212
r_mcangle_it1.076
r_angle_other_deg0.976
r_rigid_bond_restr0.897
r_mcbond_it0.775
r_mcbond_other0.303
r_symmetry_vdw_other0.271
r_nbd_other0.205
r_nbd_refined0.204
r_nbtor_refined0.176
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.109
r_nbtor_other0.083
r_chiral_restr0.072
r_bond_other_d0.008
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2756
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms35

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction