5HPA

The crystal of rhodanese domain of YgaP treated with sodium thiosulfate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52950.2 M sodium acetate in 0.1 M Tris HCl pH 8.5, and 30% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0539.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.699α = 90
b = 43.699β = 90
c = 52.28γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.127SSRLBL12-2

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
11.6637.8498.40.03734.45.313126
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)
11.661.7589.30.05716.24.2

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 REPLACEMENTTHROUGHOUT5HBO1.6637.841246064599.730.168450.167080.1974RANDOM16.007
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]
0.010.010.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.118
r_dihedral_angle_4_deg17.197
r_dihedral_angle_3_deg13.35
r_long_range_B_refined5.537
r_long_range_B_other5.169
r_dihedral_angle_1_deg5.076
r_scangle_other1.914
r_mcangle_it1.631
r_mcangle_other1.63
r_angle_refined_deg1.619
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.118
r_dihedral_angle_4_deg17.197
r_dihedral_angle_3_deg13.35
r_long_range_B_refined5.537
r_long_range_B_other5.169
r_dihedral_angle_1_deg5.076
r_scangle_other1.914
r_mcangle_it1.631
r_mcangle_other1.63
r_angle_refined_deg1.619
r_scbond_it1.194
r_scbond_other1.193
r_angle_other_deg0.959
r_mcbond_it0.945
r_mcbond_other0.939
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms794
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing