5B7S

Apo structure of Cysteine Desulfurase from Thermococcus onnurineus NA1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T3I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52870.03M MgCl2, 0.03 M CaCl2, 15% (v/v) glycerol, 15% (w/v) PEG 4000, 0.1M Tris (base)/ Bicine pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.5852.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.006α = 90
b = 92.527β = 90
c = 145.444γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-06-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.979PAL/PLS7A (6B, 6C1)

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
12.585099.90.11929.16.828968
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)
12.62.641000.4137.17.1

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 REPLACEMENTTHROUGHOUT1T3I2.5836.3627449146599.160.20780.20320.2951RANDOM52.856
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]
0.02-0.030.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.422
r_dihedral_angle_3_deg21.485
r_dihedral_angle_4_deg15.371
r_dihedral_angle_1_deg7.844
r_mcangle_it5.171
r_mcbond_it3.375
r_mcbond_other3.374
r_angle_refined_deg1.81
r_angle_other_deg1.167
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.422
r_dihedral_angle_3_deg21.485
r_dihedral_angle_4_deg15.371
r_dihedral_angle_1_deg7.844
r_mcangle_it5.171
r_mcbond_it3.375
r_mcbond_other3.374
r_angle_refined_deg1.81
r_angle_other_deg1.167
r_chiral_restr0.123
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6152
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
DENZOdata scaling
MOLREPphasing