6ABI

The apo-structure of D-lactate dehydrogenase from Fusobacterium nucleatum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J49 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298100 mM MES-Na (pH 6.0) and 1.26 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
4.8674.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.29α = 90
b = 116.29β = 90
c = 234.4γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102012-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.137.031000.1710.0460.9969.714.594385
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.211000.8310.2290.9083.213.7

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 REPLACEMENTTHROUGHOUT1J492.137.0389290471499.640.187930.186430.21665RANDOM31.673
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.94
r_dihedral_angle_4_deg26.624
r_dihedral_angle_3_deg15.198
r_long_range_B_refined7.663
r_long_range_B_other7.662
r_dihedral_angle_1_deg6.395
r_scangle_other6.235
r_scbond_it4.122
r_scbond_other4.122
r_mcangle_it3.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.94
r_dihedral_angle_4_deg26.624
r_dihedral_angle_3_deg15.198
r_long_range_B_refined7.663
r_long_range_B_other7.662
r_dihedral_angle_1_deg6.395
r_scangle_other6.235
r_scbond_it4.122
r_scbond_other4.122
r_mcangle_it3.35
r_mcangle_other3.35
r_mcbond_it2.399
r_mcbond_other2.397
r_angle_refined_deg2.102
r_angle_other_deg1.375
r_chiral_restr0.138
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.007
r_gen_planes_other0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5281
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALAdata scaling
ARP/wARPmodel building
MOLREPphasing
iMOSFLMdata reduction