1WYU

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	PEG 3350, lithium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.874	α = 90
b = 166.673	β = 90
c = 189.007	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	90	CCD	RIGAKU JUPITER 210		2004-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0000	SPring-8	BL45XU

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	2.1	50	99	0.124	15	6.9	247974	245553			16.7

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	2.1	2.18	96.2		0.673	2.6	5.7	23611

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIR	THROUGHOUT	2.1	49.57	245447	244559	12275	98.9	0.191	0.191	0.189	0.229	RANDOM	29.3

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]
6.64			-1.31		-5.34

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.5
c_scangle_it	2.95
c_scbond_it	2.09
c_mcangle_it	1.69
c_angle_deg	1.3
c_mcbond_it	1.16
c_improper_angle_d	0.83
c_bond_d	0.005
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28132
Nucleic Acid Atoms
Solvent Atoms	2145
Heterogen Atoms	60

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing