1J49

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 modelPDB 2DLDPDB ENTRY 2DLD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15pH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.4549

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.4α = 90
b = 79.4β = 90
c = 228.5γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMIRRORS1994-12-01MSINGLE 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
12.21598.70.07119.45.838147236.1
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)
2.22.2493.30.213.736.82

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 (EXCEPT FOR THE LAST 2 REFINEMENT CYCLES)PDB ENTRY 2DLD2.21537544188498.70.2090.2070.271RANDOM44.4
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_tor35.6
p_staggered_tor18.8
p_planar_tor4.3
p_mcangle_it1.5
p_scangle_it1.4
p_mcbond_it0.8
p_scbond_it0.8
p_multtor_nbd0.3
p_xhyhbond_nbd0.23
p_xyhbond_nbd0.23
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor35.6
p_staggered_tor18.8
p_planar_tor4.3
p_mcangle_it1.5
p_scangle_it1.4
p_mcbond_it0.8
p_scbond_it0.8
p_multtor_nbd0.3
p_xhyhbond_nbd0.23
p_xyhbond_nbd0.23
p_singtor_nbd0.2
p_planar_d0.033
p_chiral_restr0.03
p_plane_restr0.026
p_angle_d0.025
p_bond_d0.015
p_angle_deg
p_hb_or_metal_coord
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5207
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms93

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement