X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727850 MM AMMONIUM-N-[TRIS(HYDROXYMETHYL) - METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 4-bromobenzyl alcohol, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.2345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.05α = 90
b = 180.14β = 105.96
c = 86.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++confocal2004-04-23MSINGLE 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
11.5319.9177.20.0630.06815.45.31170706
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)
11.531.5859.20.3220.4072.72.26

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 REPLACEMENTTHROUGHOUT5vl01.5319.91168958169377.20.14880.14810.2207RANDOM21.449
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]
1.72-0.8-0.6-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.785
r_dihedral_angle_4_deg14.215
r_dihedral_angle_3_deg13.342
r_dihedral_angle_1_deg6.89
r_rigid_bond_restr3.183
r_angle_refined_deg1.895
r_angle_other_deg1.47
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.785
r_dihedral_angle_4_deg14.215
r_dihedral_angle_3_deg13.342
r_dihedral_angle_1_deg6.89
r_rigid_bond_restr3.183
r_angle_refined_deg1.895
r_angle_other_deg1.47
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.009
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 Atoms1039
Heterogen Atoms228

Software

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