3COG

Crystal structure of human cystathionase (Cystathionine gamma lyase) in complex with DL-propargylglycine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NMPPDB entry 2NMP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.32930.2M Di-ammonium hydrogen citrate, 20% PEG 3350. Streak seeding used, apo crystal soaked with inhibitor, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.35α = 90
b = 107.22β = 90
c = 153.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDouble mirrors2006-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
122092.90.1230.12313.816.7109200109200
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.198.90.4690.4453.24.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2NMP219.9110373810373854601000.160610.158310.20406RANDOM14.036
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]
-0.79-0.110.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.618
r_dihedral_angle_4_deg19.156
r_dihedral_angle_3_deg15.029
r_dihedral_angle_1_deg6.201
r_scangle_it2.896
r_scbond_it1.999
r_angle_refined_deg1.374
r_mcangle_it1.189
r_angle_other_deg0.931
r_mcbond_it0.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.618
r_dihedral_angle_4_deg19.156
r_dihedral_angle_3_deg15.029
r_dihedral_angle_1_deg6.201
r_scangle_it2.896
r_scbond_it1.999
r_angle_refined_deg1.374
r_mcangle_it1.189
r_angle_other_deg0.931
r_mcbond_it0.808
r_nbd_refined0.207
r_symmetry_hbond_refined0.201
r_nbd_other0.196
r_mcbond_other0.177
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.156
r_symmetry_vdw_other0.146
r_chiral_restr0.119
r_symmetry_vdw_refined0.107
r_nbtor_other0.089
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11836
Nucleic Acid Atoms
Solvent Atoms1160
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing