1M0N | pdb_00001m0n

Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DKA	PDB ENTRY 1DKA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.4		15% PEG 4000, 0.2-0.4 M SODIUM PYRUVATE, 0.015 M MES-KOH (PH 6.4)

Crystal Properties
Matthews coefficient	Solvent content
3.01	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.29	α = 90
b = 151.29	β = 90
c = 84.79	γ = 120

Symmetry
Space Group	P 64 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2001-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	30	96.1	0.077	18.9	3.21		28332	2	-2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.28	98.1		0.318	11.3	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1DKA	2.2	20	2	2	27846	1417	94.3	0.192	0.189	0.239	Random

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
Key	Refinement Restraint Deviation
t_dihedral_angle_d	17.3
t_angle_deg	1.957
t_bond_d	0.027
t_gen_planes	0.02
o_bond_d_na
o_bond_d_prot
o_angle_d_na
o_angle_d_prot
o_angle_deg
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d_na
o_dihedral_angle_d_prot
o_improper_angle_d
o_improper_angle_d_na
o_improper_angle_d_prot
o_mcbond_it
o_mcangle_it
o_scbond_it
o_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3252
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	27

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
TNT	refinement
CNS	phasing