3O38

Crystal structure of a short chain dehydrogenase from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IY8PDB entry 1iy8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP528953.4 mg/mL MysmA00762bA1 PS00603 against PACT B2, 0.1 M MIB buffer, 25% PEG 1500, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0439.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.81α = 90
b = 75.72β = 102.71
c = 80.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2010-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97946ALS5.0.1

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
11.955097.40.05518.923.864541-328.324
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)
11.952810.3552.9

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 REPLACEMENTTHROUGHOUTPDB entry 1iy81.955064451326597.350.1650.16240.2149RANDOM29.2692
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]
-1.620.4-0.111.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.818
r_dihedral_angle_4_deg17.465
r_dihedral_angle_3_deg12.204
r_dihedral_angle_1_deg5.758
r_scangle_it3.649
r_scbond_it2.218
r_angle_refined_deg1.355
r_mcangle_it1.305
r_mcbond_it0.764
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.818
r_dihedral_angle_4_deg17.465
r_dihedral_angle_3_deg12.204
r_dihedral_angle_1_deg5.758
r_scangle_it3.649
r_scbond_it2.218
r_angle_refined_deg1.355
r_mcangle_it1.305
r_mcbond_it0.764
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7091
Nucleic Acid Atoms
Solvent Atoms670
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction