2YPO

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound in only one site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NV8	PDB ENTRY 3NV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.969	α = 90
b = 203.969	β = 90
c = 66.6	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC CCD		2011-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2		Australian Synchrotron	MX2

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	44.16	99.9	0.1	0.102	11.5	5.3		106936		2

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	2.11	100		0.47	0.47	1.6	5.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3NV8	2	44.16	101510	5325	99.83	0.13932	0.13829	0.1593	RANDOM	28.127

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]
4.65			4.65		-9.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.655
r_dihedral_angle_4_deg	19.011
r_dihedral_angle_3_deg	14.161
r_dihedral_angle_1_deg	6.287
r_angle_refined_deg	2.002
r_angle_other_deg	1.399
r_chiral_restr	0.138
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_bond_other_d	0.007
r_gen_planes_other	0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7037
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
CCP4	phasing