5TEJ

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5 Furan Dicarboxylic and NADH


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.5150.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.059α = 90
b = 91.039β = 120.07
c = 125.922γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.4950.011000.1130.1137.74.243079
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.5399.50.4640.82.83.5

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 REPLACEMENTTHROUGHOUT1ARZ2.550.0140949209599.740.18310.18160.2117RANDOM36.786
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]
0.93-0.10.8-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.16
r_dihedral_angle_4_deg20.859
r_dihedral_angle_3_deg13.231
r_dihedral_angle_1_deg5.063
r_angle_other_deg3.719
r_mcangle_it1.851
r_angle_refined_deg1.639
r_mcbond_it1.047
r_mcbond_other1.047
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.16
r_dihedral_angle_4_deg20.859
r_dihedral_angle_3_deg13.231
r_dihedral_angle_1_deg5.063
r_angle_other_deg3.719
r_mcangle_it1.851
r_angle_refined_deg1.639
r_mcbond_it1.047
r_mcbond_other1.047
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7952
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms236

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing