3HZ4 | pdb_00003hz4

Crystal Structure of Thioredoxin from Methanosarcina mazei


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529820% Peg 3350, 0.1M Bis Tris pH 5.5, 0.2M LiSo4, 0.1M EDTA, 20% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8156.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.068α = 90
b = 82.068β = 90
c = 93.874γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMirrors2009-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9797NSLSX29A

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
12.35094.80.130.139.921.51804118041
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)
2.32.381000.399.6211639

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.350180401711292794.830.193350.190530.190.246590.24RANDOM23.48
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]
0.810.40.81-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.382
r_dihedral_angle_3_deg21.371
r_dihedral_angle_4_deg18.226
r_dihedral_angle_1_deg7.426
r_scangle_it5.763
r_scbond_it3.812
r_mcangle_it2.215
r_angle_refined_deg2.086
r_mcbond_it1.659
r_symmetry_hbond_refined0.429
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1932
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms12

Software

Software
Software NamePurpose
CBASSdata collection
SHELXmodel building
SHARPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing