4M8R

Crystal structure of a DUF4784 family protein (BACCAC_01631) from Bacteroides caccae ATCC 43185 at 2.50 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22932.00M ammonium sulfate, 0.00100M GSH (L-Glutathione reduced), GSSG (L-Glutathione oxidized), 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0759.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.084α = 90
b = 123.084β = 90
c = 269.91γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)2013-01-23MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97941,0.97871SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.533.73999.90.16613.214.14266042660
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.561001.7641.613.83114

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 DIFFRACTIONMADTHROUGHOUT2.533.73942588214899.830.20250.20150.2218RANDOM55.2499
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]
-1.13-1.13-1.133.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.016
r_dihedral_angle_4_deg18.653
r_dihedral_angle_3_deg12.967
r_dihedral_angle_1_deg6.543
r_mcangle_it3.84
r_mcbond_it2.261
r_mcbond_other2.261
r_angle_refined_deg1.355
r_angle_other_deg0.687
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.016
r_dihedral_angle_4_deg18.653
r_dihedral_angle_3_deg12.967
r_dihedral_angle_1_deg6.543
r_mcangle_it3.84
r_mcbond_it2.261
r_mcbond_other2.261
r_angle_refined_deg1.355
r_angle_other_deg0.687
r_chiral_restr0.062
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6436
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms93

Software

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