3HDU

CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (SYN_01977) FROM SYNTROPHUS ACIDITROPHICUS SB AT 2.50 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP527710.0000% MPD, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2745.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.165α = 90
b = 117.165β = 90
c = 71.602γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-01-16MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97964,0.97949SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.529.59199.90.0840.08416.87.21779960.865
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.561000.8060.8062.47.31288

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 DIFFRACTIONMADTHROUGHOUT2.529.5911776090399.890.2380.2370.257RANDOM74.556
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]
-2.23-2.234.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.122
r_dihedral_angle_3_deg11.051
r_dihedral_angle_4_deg8.167
r_dihedral_angle_1_deg2.812
r_angle_refined_deg1.415
r_angle_other_deg1.211
r_mcangle_it0.854
r_scangle_it0.547
r_mcbond_it0.504
r_scbond_it0.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.122
r_dihedral_angle_3_deg11.051
r_dihedral_angle_4_deg8.167
r_dihedral_angle_1_deg2.812
r_angle_refined_deg1.415
r_angle_other_deg1.211
r_mcangle_it0.854
r_scangle_it0.547
r_mcbond_it0.504
r_scbond_it0.353
r_nbtor_refined0.136
r_nbd_refined0.131
r_nbd_other0.119
r_symmetry_vdw_other0.091
r_chiral_restr0.081
r_mcbond_other0.079
r_symmetry_vdw_refined0.068
r_nbtor_other0.066
r_symmetry_hbond_refined0.061
r_xyhbond_nbd_refined0.054
r_bond_refined_d0.012
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3386
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
autoSHARPphasing