1J4A

INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherMODEL OF NATIVE D-LDH WHICH IS CURRENTLY BEING DEPOSITED IN THE PDB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5Orthorhombic crystals were grown by vapour diffusion from solutions of 20 % PEG 6K, 0.2 M ammonium sulphate in 0.1 M cacodylate buffer pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.9157.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.3α = 90
b = 188β = 90
c = 193.4γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1998-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.91998.40.04716.13.1132348-30.215
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)
1.91.9392.40.3272.2

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 REPLACEMENTTHROUGHOUT APART FROM THE LAST 3 CYCLESMODEL OF NATIVE D-LDH WHICH IS CURRENTLY BEING DEPOSITED IN THE PDB1.919132346664798.40.2040.2040.259RANDOM0.327
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor36.1
p_staggered_tor15
p_planar_tor3.9
p_scangle_it3.2
p_mcangle_it2.5
p_scbond_it2.5
p_mcbond_it1.9
p_multtor_nbd0.25
p_xhyhbond_nbd0.197
p_xyhbond_nbd0.197
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor36.1
p_staggered_tor15
p_planar_tor3.9
p_scangle_it3.2
p_mcangle_it2.5
p_scbond_it2.5
p_mcbond_it1.9
p_multtor_nbd0.25
p_xhyhbond_nbd0.197
p_xyhbond_nbd0.197
p_singtor_nbd0.19
p_chiral_restr0.13
p_planar_d0.035
p_angle_d0.031
p_plane_restr0.023
p_bond_d0.013
p_angle_deg
p_hb_or_metal_coord
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10473
Nucleic Acid Atoms
Solvent Atoms900
Heterogen Atoms55

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling