5B7U

Apo Structure of Cysteine Desulfurase from Thermococcus onnurineus NA1 at 1.89A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B7S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2891mM PLP, 5mM cystine, 10% (v/v) Isopropanol, 5% (w/v) PEG 8000, Imidazol/HCl pH 5.9
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.488α = 90
b = 62.789β = 90
c = 171.317γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-03-31MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.97PAL/PLS5C (4A)

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
11.950970.06254.029.666011
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)
11.91.9391.90.30699.6

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 REPLACEMENTTHROUGHOUT5B7S1.946.17762613332696.950.167510.16560.20309RANDOM23.938
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.865
r_dihedral_angle_4_deg17.662
r_dihedral_angle_3_deg14.647
r_dihedral_angle_1_deg6.232
r_long_range_B_refined6.149
r_long_range_B_other6.093
r_scangle_other5.069
r_scbond_it3.362
r_scbond_other3.362
r_mcangle_it2.635
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.865
r_dihedral_angle_4_deg17.662
r_dihedral_angle_3_deg14.647
r_dihedral_angle_1_deg6.232
r_long_range_B_refined6.149
r_long_range_B_other6.093
r_scangle_other5.069
r_scbond_it3.362
r_scbond_other3.362
r_mcangle_it2.635
r_mcangle_other2.635
r_mcbond_it2.046
r_mcbond_other2.04
r_angle_refined_deg1.896
r_angle_other_deg1.078
r_chiral_restr0.132
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
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 Atoms6286
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing