Experiment: 2DTT

Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 complexed with (1'R,2'S)-biopterin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DJ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbathch	6.25	291	16.5% PEG 20000, 0.1M Acetate, NAOH pH6.25, 3mM Biopterin, microbathch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.682	α = 90
b = 105.445	β = 90.95
c = 96.147	γ = 90

Symmetry
Space Group	P 1 21 1

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	mirrors	2006-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	50	90.4	0.072	0.067	8.3	3	36076	32611			32.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	81.4		0.229	0.225	3.1	3	2906

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2DJ6	2.2	35.68	36076	32611	1637	90.4	0.195	0.195	0.1918	0.236	0.2336	RANDOM	38.8

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]
3.25		-6.17	2.24		-5.48

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_angle_deg	1.3
c_improper_angle_d	0.65
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5403
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	102

Software

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