3BRS

Crystal structure of sugar transporter from Clostridium phytofermentans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52940.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, cryoprotected in 20% Glycerol, VAPOR DIFFUSION, temperature 294K, pH 5.50
Crystal Properties
Matthews coefficientSolvent content
2.4349.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.62α = 90
b = 54.7β = 111.78
c = 90.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

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
125097.90.1093.92.480628
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)
122.0797.40.442.2

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 DIFFRACTIONSADTHROUGHOUT219.6839783212199.220.207440.203390.28284RANDOM37.538
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]
0.02-0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.021
r_dihedral_angle_3_deg20.163
r_scbond_it13.773
r_dihedral_angle_4_deg12.008
r_dihedral_angle_1_deg8.299
r_scangle_it6.955
r_mcangle_it6.485
r_mcbond_it2.326
r_angle_refined_deg2.313
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.021
r_dihedral_angle_3_deg20.163
r_scbond_it13.773
r_dihedral_angle_4_deg12.008
r_dihedral_angle_1_deg8.299
r_scangle_it6.955
r_mcangle_it6.485
r_mcbond_it2.326
r_angle_refined_deg2.313
r_nbtor_refined0.32
r_symmetry_vdw_refined0.248
r_nbd_refined0.244
r_xyhbond_nbd_refined0.231
r_chiral_restr0.186
r_symmetry_hbond_refined0.085
r_bond_refined_d0.027
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms4208
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXDphasing