1M0O | pdb_00001m0o

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

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, 0.20 - 0.40 M SODIUM PYRUVATE, 0.015 M MES-KOH (pH 6.4)

Crystal Properties
Matthews coefficient	Solvent content
3.12	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.84	α = 90
b = 152.84	β = 90
c = 86.36	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	298	IMAGE PLATE	RIGAKU RAXIS IV		2001-05-12	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	2.4	30	100	0.087	10.7	9.1	23748	23748	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)
	2.4	2.49	100		0.349	10.1	7.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2.4	20	2	23728	1187	99.9	0.144	0.139	0.201	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	17.7
t_angle_deg	1.78
t_trig_c_planes	0.16
t_bond_d	0.024
t_gen_planes	0.019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3252
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	26

Software

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