5J6F

Crystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	298	A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 and 0.2 mM chorismic acid. 2 ??L drop size. 500 ??L reservoir volume.

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.438	α = 90
b = 95.438	β = 90
c = 167.452	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315r		2012-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953700	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.75	82.65	99.9	0.079	1	18	7.6		22482

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	2.75	2.88	100		1.336		7.7

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	3TFC	2.75	82.65	21178	1054	99.02	0.18471	0.18221	0.2352	RANDOM	77.759

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]
-0.49	-0.24		-0.49		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.677
r_dihedral_angle_3_deg	18.841
r_dihedral_angle_4_deg	16.568
r_long_range_B_other	7.983
r_long_range_B_refined	7.981
r_dihedral_angle_1_deg	6.922
r_scangle_other	6.26
r_mcangle_it	4.289
r_mcangle_other	4.289
r_scbond_it	3.895
r_scbond_other	3.894
r_mcbond_it	2.729
r_mcbond_other	2.726
r_angle_refined_deg	2.12
r_angle_other_deg	1.511
r_chiral_restr	0.107
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5366
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction