2IHU

Carboxyethylarginine synthase from Streptomyces clavuligerus: putative reaction intermediate complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42901.6 M (NH4)2SO4, 0.1 M HEPES pH 7.4, 10 mg/mL protein with 3-fold excess of ThDP, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.0960.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.691α = 90
b = 127.863β = 90
c = 197.15γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.813EMBL/DESY, HAMBURGX11

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
12.0528.13397.10.0790.0797.93.718909318360920.17
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)
12.052.1688.90.3050.3052.43.3

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 1UPA2.0528.13189263174698883096.970.172460.1710.20092RANDOM20.712
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]
1.89-0.75-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.216
r_dihedral_angle_4_deg13.781
r_dihedral_angle_3_deg12.421
r_dihedral_angle_1_deg5.786
r_scangle_it1.803
r_angle_refined_deg1.206
r_scbond_it1.095
r_mcangle_it0.701
r_mcbond_it0.383
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.216
r_dihedral_angle_4_deg13.781
r_dihedral_angle_3_deg12.421
r_dihedral_angle_1_deg5.786
r_scangle_it1.803
r_angle_refined_deg1.206
r_scbond_it1.095
r_mcangle_it0.701
r_mcbond_it0.383
r_nbtor_refined0.301
r_nbd_refined0.192
r_metal_ion_refined0.123
r_symmetry_vdw_refined0.122
r_xyhbond_nbd_refined0.118
r_symmetry_hbond_refined0.111
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16649
Nucleic Acid Atoms
Solvent Atoms1405
Heterogen Atoms171

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACphasing