3U0B

Crystal structure of an oxidoreductase from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LLS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293MysmA.00010.a at 29.8 mg/ml, 25% PEG 1500, 0.1 M MMT, pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
237

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.73α = 90
b = 58.22β = 127.82
c = 76.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSaturn 944+2010-05-10SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5

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
11.75098.80.05328.8339290-316.838
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)
11.71.7493.60.1935.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3LLS1.747.3139260197599.170.1380.1370.162RANDOM12.175
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]
-0.31-0.240.32-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.709
r_dihedral_angle_4_deg18.502
r_dihedral_angle_3_deg10.495
r_dihedral_angle_1_deg5.721
r_scangle_it2.808
r_scbond_it1.785
r_angle_other_deg1.572
r_angle_refined_deg1.505
r_mcangle_it0.823
r_mcbond_it0.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.709
r_dihedral_angle_4_deg18.502
r_dihedral_angle_3_deg10.495
r_dihedral_angle_1_deg5.721
r_scangle_it2.808
r_scbond_it1.785
r_angle_other_deg1.572
r_angle_refined_deg1.505
r_mcangle_it0.823
r_mcbond_it0.434
r_chiral_restr0.094
r_mcbond_other0.065
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3008
Nucleic Acid Atoms
Solvent Atoms562
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction