4ITX

P113S mutant of E. coli Cystathionine beta-lyase MetC inhibited by reaction with L-Ala-P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CL1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.229320% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.97α = 90
b = 153.126β = 90
c = 150.835γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plateosmic2011-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6119.499.911.68982889828
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.6993.79.7

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1CL11.6119.48115381153428095.420.163250.163250.161540.19532RANDOM11.541
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]
0.05-0.04-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.111
r_dihedral_angle_4_deg24.257
r_dihedral_angle_3_deg12.366
r_dihedral_angle_1_deg6.639
r_scangle_it4.339
r_scbond_it2.884
r_angle_refined_deg2.02
r_mcangle_it1.879
r_mcbond_it1.251
r_angle_other_deg1.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.111
r_dihedral_angle_4_deg24.257
r_dihedral_angle_3_deg12.366
r_dihedral_angle_1_deg6.639
r_scangle_it4.339
r_scbond_it2.884
r_angle_refined_deg2.02
r_mcangle_it1.879
r_mcbond_it1.251
r_angle_other_deg1.149
r_mcbond_other0.47
r_chiral_restr0.209
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5996
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms46

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling