8SF4 | pdb_00008sf4

Cystathionine gamma lyase from Thermobifida fusca in internal aldimine form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5X5H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Well solution comprising 20-30% PEG300, 0.1 M HEPES, 0.2 M MgCl2. 2 uL drops were laid with a 1:1 mixture of well solution and 8 mg/mL protein in 0.1 M HEPES buffer pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.2462.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.591α = 90
b = 117.591β = 90
c = 117.591γ = 90
Symmetry
Space GroupP 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2021-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.978720APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.45540.0031000.075125.3622.194728
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.491001.6970.7482.0921.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.45540.00394728468799.9640.1340.1330.130.14810.1520.789
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.09
r_dihedral_angle_4_deg20.121
r_dihedral_angle_3_deg11.996
r_dihedral_angle_1_deg6.581
r_lrange_it5.077
r_lrange_other4.916
r_scangle_other2.842
r_scangle_it2.832
r_angle_refined_deg2.248
r_scbond_it1.994
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.09
r_dihedral_angle_4_deg20.121
r_dihedral_angle_3_deg11.996
r_dihedral_angle_1_deg6.581
r_lrange_it5.077
r_lrange_other4.916
r_scangle_other2.842
r_scangle_it2.832
r_angle_refined_deg2.248
r_scbond_it1.994
r_scbond_other1.959
r_angle_other_deg1.679
r_mcangle_other1.325
r_mcangle_it1.324
r_mcbond_it0.96
r_mcbond_other0.943
r_symmetry_xyhbond_nbd_other0.282
r_symmetry_xyhbond_nbd_refined0.231
r_nbd_refined0.227
r_xyhbond_nbd_other0.223
r_nbtor_refined0.173
r_nbd_other0.173
r_symmetry_nbd_other0.172
r_symmetry_nbd_refined0.164
r_xyhbond_nbd_refined0.136
r_chiral_restr0.118
r_symmetry_nbtor_other0.089
r_metal_ion_refined0.038
r_bond_refined_d0.02
r_gen_planes_refined0.015
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2835
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing