3FEM

Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase from Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	4M formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
4.81	74.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.073	α = 90
b = 154.218	β = 90
c = 154.868	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	ADSC QUANTUM 4	TOROIDAL (ESRF)	2007-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	3.02	20	99.8	0.075	23.4	7.9	72026	72026		-4	79.3

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	3.02	3.05	96.2		0.416	3.4	6.5

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	2NV1	3.02	20	71521	69465	2053	99.66	0.16267	0.16215	0.22	0.18097	0.22	RANDOM	32.98

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]
-8.08			-9.07		17.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.96
r_dihedral_angle_3_deg	23.629
r_dihedral_angle_4_deg	22.197
r_dihedral_angle_1_deg	6.408
r_scangle_it	3.581
r_mcangle_it	2.644
r_scbond_it	2.269
r_mcbond_it	1.372
r_angle_refined_deg	1.284
r_angle_other_deg	0.894
r_symmetry_vdw_other	0.377
r_symmetry_vdw_refined	0.294
r_nbd_refined	0.278
r_mcbond_other	0.25
r_nbd_other	0.225
r_nbtor_refined	0.194
r_xyhbond_nbd_refined	0.186
r_nbtor_other	0.098
r_chiral_restr	0.063
r_xyhbond_nbd_other	0.054
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12594
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling