1XW4

Crystal Structure of Human Sulfiredoxin (Srx) in Complex with ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5293MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.956.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.451α = 90
b = 68.451β = 90
c = 50.891γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUCONFOCAL BLUE MAX-FLUX2004-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
1229.6499.60.05130.99.639562
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0795.34.45.03

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1XW3229.69602908445699.430.220680.218250.27084RANDOM27.872
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]
0.540.270.54-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.158
r_dihedral_angle_4_deg14.855
r_dihedral_angle_3_deg14.42
r_dihedral_angle_1_deg6.479
r_scangle_it4.357
r_scbond_it2.778
r_mcangle_it1.834
r_angle_refined_deg1.828
r_mcbond_it1.126
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.158
r_dihedral_angle_4_deg14.855
r_dihedral_angle_3_deg14.42
r_dihedral_angle_1_deg6.479
r_scangle_it4.357
r_scbond_it2.778
r_mcangle_it1.834
r_angle_refined_deg1.828
r_mcbond_it1.126
r_nbtor_refined0.301
r_symmetry_vdw_refined0.24
r_xyhbond_nbd_refined0.224
r_nbd_refined0.216
r_chiral_restr0.115
r_symmetry_hbond_refined0.108
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms840
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
CNSrefinement
CNSphasing
d*TREKdata scaling