1DXL | pdb_00001dxl

Dihydrolipoamide dehydrogenase of glycine decarboxylase from Pisum Sativum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LAD	PDB ENTRY 3LAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		15 % PEG MME 5K, 100 MM MES PH 5, 0.45 % HEPTYL-B-D-THIOGLUCOPYRANOSIDE, 2MM POTASSIUM LIPOATE.

Crystal Properties
Matthews coefficient	Solvent content
2.76	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.56	α = 90
b = 108.33	β = 90
c = 202.19	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	MULTILAYER MIRRORS	1998-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.15	30	87	0.063	8.6	3.4		33527			87.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.32	77.3		0.254	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3LAD	3.15	15	33219	1650	86.1	0.226	0.226	0.323	RANDOM	75

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]
4.63			-11.76		7.13

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.5
c_angle_deg	2.1
c_improper_angle_d	1.2
c_bond_d	0.019
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13900
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	212

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing