3BWX

Crystal structure of an alpha/beta hydrolase (YP_496220.1) from Novosphingobium aromaticivorans DSM 12444 at 1.50 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.1277NANODROP, 0.2M CaCl2, 20.0% PEG 3350, No Buffer pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
238.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.48α = 90
b = 69.95β = 90
c = 82.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2007-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97908SSRLBL11-1

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
11.527.71498.80.1057.841517-311.671
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)
11.51.5597.40.7041.5

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 DIFFRACTIONSADTHROUGHOUT1.527.71441469209599.070.1630.1610.203RANDOM11.006
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]
-0.40.46-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.231
r_dihedral_angle_4_deg18.191
r_dihedral_angle_3_deg12.551
r_dihedral_angle_1_deg5.775
r_scangle_it5.445
r_scbond_it4.065
r_mcangle_it2.605
r_mcbond_it2.061
r_angle_refined_deg1.671
r_angle_other_deg1.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.231
r_dihedral_angle_4_deg18.191
r_dihedral_angle_3_deg12.551
r_dihedral_angle_1_deg5.775
r_scangle_it5.445
r_scbond_it4.065
r_mcangle_it2.605
r_mcbond_it2.061
r_angle_refined_deg1.671
r_angle_other_deg1.041
r_mcbond_other0.526
r_symmetry_vdw_other0.28
r_symmetry_vdw_refined0.24
r_nbd_refined0.221
r_nbd_other0.211
r_symmetry_hbond_refined0.204
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.166
r_chiral_restr0.096
r_metal_ion_refined0.091
r_nbtor_other0.087
r_symmetry_metal_ion_refined0.02
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2185
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing