3LUB

Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.32770.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1743.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.906α = 90
b = 156.79β = 95.29
c = 170.161γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
12.1143.03399.80.1228.253.8167009-325.198
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)
2.112.1999.90.5972.1

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 DIFFRACTIONSADTHROUGHOUT2.1143.033166973860499.830.1530.1510.193THIN SHELLS25.45
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]
1.720.31-0.33-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.198
r_dihedral_angle_3_deg13.078
r_dihedral_angle_4_deg11.312
r_dihedral_angle_1_deg5.912
r_scangle_it5.691
r_scbond_it4.25
r_mcangle_it2.242
r_mcbond_it1.631
r_angle_refined_deg1.416
r_angle_other_deg0.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.198
r_dihedral_angle_3_deg13.078
r_dihedral_angle_4_deg11.312
r_dihedral_angle_1_deg5.912
r_scangle_it5.691
r_scbond_it4.25
r_mcangle_it2.242
r_mcbond_it1.631
r_angle_refined_deg1.416
r_angle_other_deg0.955
r_mcbond_other0.23
r_symmetry_vdw_refined0.209
r_symmetry_vdw_other0.202
r_nbd_refined0.193
r_nbd_other0.188
r_nbtor_refined0.175
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.163
r_metal_ion_refined0.1
r_chiral_restr0.086
r_nbtor_other0.085
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_xyhbond_nbd_other0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23844
Nucleic Acid Atoms
Solvent Atoms2223
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing