3DUE

CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527735.0000% 2-ethoxyethanol, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1542.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.601α = 90
b = 50.874β = 90
c = 79.507γ = 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)2008-06-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97926,0.97876SSRLBL11-1

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
11.8529.3611000.1090.1095.43.51151917.91
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)
11.851.91000.5880.5881.33.6

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 DIFFRACTIONMADTHROUGHOUT1.8529.3611093154999.960.194320.192340.23321RANDOM19.076
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]
-0.710.680.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.168
r_dihedral_angle_3_deg10.88
r_dihedral_angle_4_deg5.69
r_dihedral_angle_1_deg4.367
r_scangle_it2.237
r_mcangle_it1.964
r_angle_refined_deg1.654
r_scbond_it1.502
r_mcbond_it1.422
r_angle_other_deg0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.168
r_dihedral_angle_3_deg10.88
r_dihedral_angle_4_deg5.69
r_dihedral_angle_1_deg4.367
r_scangle_it2.237
r_mcangle_it1.964
r_angle_refined_deg1.654
r_scbond_it1.502
r_mcbond_it1.422
r_angle_other_deg0.94
r_mcbond_other0.343
r_xyhbond_nbd_other0.335
r_symmetry_vdw_refined0.25
r_symmetry_vdw_other0.244
r_nbd_refined0.212
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.194
r_nbd_other0.193
r_nbtor_refined0.184
r_chiral_restr0.106
r_nbtor_other0.089
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1019
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms5

Software

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