1B04

STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.665

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.72α = 90
b = 95.72β = 90
c = 225.89γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.82097.50.098.92.825982
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.999.20.308

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRTHROUGHOUT2.82025982130197.40.230.230.31RANDOM47.4
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_tor32.4
p_staggered_tor24.6
p_special_tor15
p_planar_tor4.3
p_scangle_it4.057
p_mcangle_it3.6
p_scbond_it2.462
p_mcbond_it2.122
p_multtor_nbd0.282
p_singtor_nbd0.221
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor32.4
p_staggered_tor24.6
p_special_tor15
p_planar_tor4.3
p_scangle_it4.057
p_mcangle_it3.6
p_scbond_it2.462
p_mcbond_it2.122
p_multtor_nbd0.282
p_singtor_nbd0.221
p_xyhbond_nbd0.218
p_chiral_restr0.193
p_planar_d0.061
p_angle_d0.056
p_plane_restr0.0266
p_bond_d0.016
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4936
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling