5B87

Crystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex with alanine at 2.3 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52890.03 M MgCl2, 0.03 M CaCl2, 15% (v/v) glycerol, 15% (w/v) PEG 4000, 5mM L-alanine, 1mM PLP and 0.1 M Tris (base)/ Bicine pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.5652.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.282α = 90
b = 93.809β = 90
c = 145.534γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-07-11MMAD
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
12.285095.50.09534.66.440955
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)
12.282.321000.385.36.1

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 REPLACEMENTTHROUGHOUT5B7S2.2849.438845204095.90.1850.1830.232RANDOM43.09
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]
-0.254.47-4.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.107
r_dihedral_angle_3_deg20.714
r_dihedral_angle_4_deg15.378
r_long_range_B_other8.405
r_long_range_B_refined8.404
r_dihedral_angle_1_deg6.897
r_scangle_other6.809
r_mcangle_it4.91
r_mcangle_other4.91
r_scbond_other4.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.107
r_dihedral_angle_3_deg20.714
r_dihedral_angle_4_deg15.378
r_long_range_B_other8.405
r_long_range_B_refined8.404
r_dihedral_angle_1_deg6.897
r_scangle_other6.809
r_mcangle_it4.91
r_mcangle_other4.91
r_scbond_other4.48
r_scbond_it4.479
r_mcbond_it3.452
r_mcbond_other3.451
r_angle_refined_deg2.03
r_angle_other_deg1.246
r_chiral_restr0.161
r_bond_refined_d0.017
r_gen_planes_refined0.009
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 Atoms6218
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms42

Software

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