3O0L

Crystal structure of a Pfam DUF1425 family member (Shew_1734) from Shewanella sp. pv-4 at 1.81 a resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.142931.4100M ammonium sulfate, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.14, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7355.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.633α = 90
b = 62.633β = 90
c = 119.04γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2010-06-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97920,0.97860SSRLBL11-1

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
11.8129.7699.90.06513.16253522535231.397
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)
11.811.861000.740.742.26.11835

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 DIFFRACTIONMADTHROUGHOUT1.8129.7625123127699.10.20520.20410.2275RANDOM38.988
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]
0.950.470.95-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.376
r_dihedral_angle_4_deg16.592
r_dihedral_angle_3_deg13.62
r_scangle_it7.853
r_dihedral_angle_1_deg5.547
r_scbond_it5.466
r_mcangle_it3.612
r_mcbond_it2.123
r_angle_refined_deg1.608
r_angle_other_deg0.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.376
r_dihedral_angle_4_deg16.592
r_dihedral_angle_3_deg13.62
r_scangle_it7.853
r_dihedral_angle_1_deg5.547
r_scbond_it5.466
r_mcangle_it3.612
r_mcbond_it2.123
r_angle_refined_deg1.608
r_angle_other_deg0.896
r_mcbond_other0.585
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1655
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms12

Software

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