3PZL

The crystal structure of agmatine ureohydrolase of Thermoplasma volcanium


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92910.1 M BICINE pH 9.0, 2% v/v 1,4-Dioxane, 10% w/v PEG 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4449.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.139α = 90
b = 95.139β = 90
c = 198.375γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2010-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9792NSLSX25

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
12.783.493.940.12415.720.62614664.2
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)
2.72.851000.684.421.34199

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.782.3926146139893.940.222080.219540.27105RANDOM59.624
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]
2.481.242.48-3.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.183
r_dihedral_angle_4_deg18.9
r_dihedral_angle_3_deg16.728
r_dihedral_angle_1_deg6.444
r_scangle_it3.869
r_scbond_it2.538
r_mcangle_it1.522
r_angle_refined_deg1.373
r_mcbond_it0.972
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.183
r_dihedral_angle_4_deg18.9
r_dihedral_angle_3_deg16.728
r_dihedral_angle_1_deg6.444
r_scangle_it3.869
r_scbond_it2.538
r_mcangle_it1.522
r_angle_refined_deg1.373
r_mcbond_it0.972
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6840
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms6

Software

Software
Software NamePurpose
CBASSdata collection
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling