2V6B

Crystal structure of lactate dehydrogenase from Deinococcus Radiodurans (apo form)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
190.1M BICINE PH 9, 20% PEG 5K MME
Crystal Properties
Matthews coefficientSolvent content
2.2445.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.35α = 90
b = 127.93β = 90
c = 72.92γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.52098.90.0617.064.3540233-341.6
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)
12.52.5594.60.463.124.28

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 1LDN2.519.8340233201299.10.230.230.25RANDOM51
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]
2.35-5.453.1
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.1
c_scangle_it4.34
c_mcangle_it3.32
c_scbond_it2.97
c_mcbond_it2.03
c_angle_deg1.1
c_improper_angle_d0.89
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.1
c_scangle_it4.34
c_mcangle_it3.32
c_scbond_it2.97
c_mcbond_it2.03
c_angle_deg1.1
c_improper_angle_d0.89
c_bond_d0.008
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 Atoms8218
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing