4A8H

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A1SPDB ENTRY 1A1S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5125 MM AMMONIUM SULPHATE, 17% PEG 3350, 0.1 M BIS-TRIS PH 5.5, 0.43 MM N-(PHOSPHONOACETYL)PUTRESCINE
Crystal Properties
Matthews coefficientSolvent content
2.9157

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.2α = 90
b = 117.2β = 90
c = 225.345γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2006-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

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
12.5461000.1235.121.332509236.5
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)
12.5201000.439.521.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1A1S2.5293077916371000.1840.182250.21651RANDOM19.296
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]
-0.19-0.1-0.190.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.861
r_dihedral_angle_4_deg17.682
r_dihedral_angle_3_deg13.016
r_dihedral_angle_1_deg5.367
r_scangle_it1.604
r_angle_refined_deg1.165
r_scbond_it1.013
r_angle_other_deg0.874
r_mcangle_it0.541
r_mcbond_it0.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.861
r_dihedral_angle_4_deg17.682
r_dihedral_angle_3_deg13.016
r_dihedral_angle_1_deg5.367
r_scangle_it1.604
r_angle_refined_deg1.165
r_scbond_it1.013
r_angle_other_deg0.874
r_mcangle_it0.541
r_mcbond_it0.271
r_chiral_restr0.078
r_mcbond_other0.063
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5380
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing