3O05

Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Complxed with Substrate PLP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	20% PEG 400, 0.1M Megnesium Cloride, 0.1M HEPES, 2.5mM PLP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.972	α = 90
b = 109.421	β = 90
c = 155.389	γ = 90

Symmetry
Space Group	P 2 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	273	CCD	RAYONIX MX-225		2009-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.0	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	32.4	99.2			51330	51330	2	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	97.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	1znn	2.2	32.4	51330	48770	2625	98.87	0.19563	0.19399	0.2274	RANDOM	44.336

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]
1.19			-0.51		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.36
r_dihedral_angle_4_deg	23.463
r_dihedral_angle_3_deg	15.862
r_scangle_it	13.295
r_scbond_it	8.964
r_mcangle_it	6.345
r_dihedral_angle_1_deg	5.275
r_mcbond_it	4.672
r_angle_refined_deg	1.095
r_nbtor_refined	0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.36
r_dihedral_angle_4_deg	23.463
r_dihedral_angle_3_deg	15.862
r_scangle_it	13.295
r_scbond_it	8.964
r_mcangle_it	6.345
r_dihedral_angle_1_deg	5.275
r_mcbond_it	4.672
r_angle_refined_deg	1.095
r_nbtor_refined	0.325
r_symmetry_hbond_refined	0.301
r_symmetry_vdw_refined	0.298
r_nbd_refined	0.246
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5871
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.