7LOL

The structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NPI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2291Agmatinase at 12 mg/mL in Buffer 25 mM Tris-HCl pH 8.0, 2 mM MnCl2. Condition: 0.1 M phosphate/citrate pH 4.2 and 40% PEG 300
Crystal Properties
Matthews coefficientSolvent content
1.9938.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.746α = 90
b = 81.746β = 90
c = 207.436γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.835.7999.870.065760.0675328.7619.92515427.14
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8640.8920.91613.61

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3NPI1.835.791.3425127124499.890.17130.17010.194733.35
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
f_dihedral_angle_d16.9009
f_angle_d1.3536
f_chiral_restr0.091
f_bond_d0.0145
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2256
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms24

Software

Software
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
BALBESphasing
Cootmodel building