3MNG

wild type human PrxV with DTT bound as a competitive inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6298Reservoir contained 1.6 M ammonium sulfate, 0.1 M sodium citrate, 0.2 M sodium/potassium tartrate. Protein was stored at 0.8 mM with 10 mM DTT., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.8367.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.313α = 90
b = 67.313β = 90
c = 123.867γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.978ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.455999.980.09430.936.748609
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.451.531000.3936.9147365

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 DIFFRACTIONRigid body refinement of starting modelTHROUGHOUTpdb code 1HD2 with benzoate removed1.455948609263399.980.114220.113030.13618RANDOM11.049
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]
-0.29-0.290.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.523
r_dihedral_angle_4_deg11.064
r_dihedral_angle_3_deg10.911
r_scangle_it9.969
r_scbond_it6.9
r_dihedral_angle_1_deg6.104
r_mcangle_it4.357
r_mcbond_it3.104
r_rigid_bond_restr2.816
r_angle_refined_deg2.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.523
r_dihedral_angle_4_deg11.064
r_dihedral_angle_3_deg10.911
r_scangle_it9.969
r_scbond_it6.9
r_dihedral_angle_1_deg6.104
r_mcangle_it4.357
r_mcbond_it3.104
r_rigid_bond_restr2.816
r_angle_refined_deg2.726
r_angle_other_deg2.413
r_mcbond_other1.081
r_chiral_restr0.161
r_gen_planes_refined0.013
r_bond_refined_d0.012
r_gen_planes_other0.001
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1190
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing