1M0P

Structure of Dialkylglycine Decarboxylase Complexed with 1-Amino-1-phenylethanephosphonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DKAPDB ENTRY 1DKA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.415% PEG 4000, 0.20 - 0.40 M SODIUM PYRUVATE, 0.015 M MES-KOH (pH 6.4)
Crystal Properties
Matthews coefficientSolvent content
2.9861

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.77α = 90
b = 150.77β = 90
c = 84.63γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2001-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.63093.80.08211.53.316888168882-2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6992.40.3069.13.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1DKA2.62021658084492.10.1780.1730.23random
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_d18.73
t_angle_deg2.067
t_gen_planes0.18
t_bond_d0.03
t_trig_c_planes0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3252
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms30

Software

Software
Software NamePurpose
TNTrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing