X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MDOPDB entry 1MDO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch6.529850 mM MES, 10% PEG 8000, 1 mM PLP, 1 mM alpha-ketoglutarate, 50 mM NaCl, pH 6.5, batch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.271α = 90
b = 152.933β = 102.09
c = 105.726γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUMmontell optics2007-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.83098.50.0816.868.5114410314198722
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)
11.81.996.10.363.443.5521555

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1MDO1.8301439321419811417598.50.1790.1790.1760.253random22.291
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
t_dihedral_angle_d17
t_angle_deg1.9
t_bond_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11320
Nucleic Acid Atoms
Solvent Atoms1042
Heterogen Atoms23

Software

Software
Software NamePurpose
PHASERphasing
DMphasing
TNTrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
SADABSdata scaling