X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VL0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727810 mg/ml protein, 1 mM NAD+, 4 mM 1H,1H-heptafluorobutanol, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethananesulfonate, 10-25% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.2448.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.15α = 90
b = 180.27β = 105.83
c = 86.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORRIGAKUconfocal2004-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.5519.9288.30.0490.05320.75.64188871
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6177.20.2790.3463.12.62

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 REPLACEMENTTHROUGHOUT5VL01.5519.84187028176988.260.13820.13770.1923RANDOM20.908
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]
1.290.06-0.97-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.655
r_dihedral_angle_4_deg13.303
r_dihedral_angle_3_deg12.6
r_dihedral_angle_1_deg6.854
r_rigid_bond_restr3.498
r_angle_refined_deg1.977
r_angle_other_deg1.504
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.655
r_dihedral_angle_4_deg13.303
r_dihedral_angle_3_deg12.6
r_dihedral_angle_1_deg6.854
r_rigid_bond_restr3.498
r_angle_refined_deg1.977
r_angle_other_deg1.504
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11140
Nucleic Acid Atoms
Solvent Atoms1238
Heterogen Atoms296

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction
REFMACphasing