3K5P

Crystal structure of amino acid-binding ACT: D-isomer specific 2-hydroxyacid dehydrogenase catalytic domain from Brucella melitensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P9C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP628928 mg/mL protein in 25 mM Hepes pH 7, 0.3 M NaCl, 10% glycerol against Cryo Full condition B3: 50% PEG 400, 5% PEG 1000, 10% glycerol, 0.1 M MES pH 6.0, crystal tracking ID 204157b3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9157.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.891α = 90
b = 97.891β = 90
c = 189.215γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.1538.68397.50.0933.217.329302
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)
12.152.23820.5543.287.72412

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 REPLACEMENTTHROUGHOUT2p9c2.1538.68329249148597.520.1840.1820.216RANDOM33.332
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]
0.610.310.61-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.747
r_dihedral_angle_4_deg14.715
r_dihedral_angle_3_deg13.216
r_dihedral_angle_1_deg5.6
r_scangle_it3.561
r_scbond_it2.161
r_angle_refined_deg1.385
r_mcangle_it1.247
r_mcbond_it0.676
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.747
r_dihedral_angle_4_deg14.715
r_dihedral_angle_3_deg13.216
r_dihedral_angle_1_deg5.6
r_scangle_it3.561
r_scbond_it2.161
r_angle_refined_deg1.385
r_mcangle_it1.247
r_mcbond_it0.676
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3028
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms22

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling