3GZS

Crystal structure of a susd superfamily protein (bf3413) from bacteroides fragilis nctc 9343 at 2.10 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.43293NANODROP, 25.0% PEG 3000, 0.1M Sodium acetate pH 4.43, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.921α = 90
b = 50.377β = 108.05
c = 117.95γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror, vertical and horizontal focusing mirrors2009-01-28MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.91837, 0.97946, 0.97907SSRLBL12-2

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
12.0929.6393.20.04157418-337.054
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)
12.092.1677.90.4032

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 DIFFRACTIONMADTHROUGHOUT2.0929.6357418293497.270.1580.1560.198RANDOM51.818
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]
0.810.3-0.43-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.557
r_dihedral_angle_4_deg11.981
r_dihedral_angle_3_deg10.288
r_scangle_it5.217
r_scbond_it4.052
r_dihedral_angle_1_deg3.357
r_mcangle_it2.283
r_mcbond_it1.598
r_angle_refined_deg1.157
r_angle_other_deg0.983
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.557
r_dihedral_angle_4_deg11.981
r_dihedral_angle_3_deg10.288
r_scangle_it5.217
r_scbond_it4.052
r_dihedral_angle_1_deg3.357
r_mcangle_it2.283
r_mcbond_it1.598
r_angle_refined_deg1.157
r_angle_other_deg0.983
r_mcbond_other0.401
r_symmetry_hbond_refined0.218
r_nbd_refined0.201
r_symmetry_vdw_other0.199
r_nbtor_refined0.181
r_symmetry_vdw_refined0.181
r_nbd_other0.17
r_xyhbond_nbd_refined0.17
r_chiral_restr0.087
r_nbtor_other0.086
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7734
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms64

Software

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