3WSW

Crystal structure of minor L-lactate dehydrogenase from Enterococcus mundtii in the ligands-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LDNPDB ENTRY 1LDN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.32986%(w/v) PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4149.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.77α = 90
b = 123.54β = 107.75
c = 85.79γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252010-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0000SPring-8BL26B2

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
12.310097.30.1078.22.9579635796314.4
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)
12.32.4297.40.4132.42.88475

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 1LDN2.329.6725563555635282993.10.1950.1950.246RANDOM33.3
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]
24.476.65-15.71-8.75
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.3
c_scangle_it2.93
c_mcangle_it2.03
c_scbond_it2.02
c_mcbond_it1.26
c_angle_deg1.2
c_improper_angle_d0.73
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.3
c_scangle_it2.93
c_mcangle_it2.03
c_scbond_it2.02
c_mcbond_it1.26
c_angle_deg1.2
c_improper_angle_d0.73
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9655
Nucleic Acid Atoms
Solvent Atoms507
Heterogen Atoms234

Software

Software
Software NamePurpose
BSSdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling