4ZND | pdb_00004znd

2.55 Angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA) from Coxiella burnetii in complex with shikimate-3-phosphate, phosphate, and potassium

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Protein solution: 7.5 mg/ml, 0.25 M NaCl, 0.01 M Tris-HCl pH 8.3 Crystallization condition: Classics II F8 (Qiagen): 0.2 M Ammonium sulfate, 0.1 m Hepes pH 7.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.795	α = 90
b = 94.795	β = 90
c = 233.668	γ = 120

Symmetry
Space Group	P 61 2 2

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	MARMOSAIC 300 mm CCD		2011-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97850	APS	21-ID-D

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	2.55	30	99.2	0.089	16.8	6.3		21004

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	2.55	2.59	100		0.538	3.6	6.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3SLH	2.55	29.99	19891	1007	99.09	0.16892	0.16553	0.17	0.23801	0.24	RANDOM	61.513

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]
0.45	0.23		0.45		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.161
r_dihedral_angle_4_deg	21.887
r_dihedral_angle_3_deg	17.8
r_long_range_B_refined	9.966
r_dihedral_angle_1_deg	7.366
r_scbond_it	5.835
r_mcangle_it	5.542
r_mcbond_it	3.947
r_angle_refined_deg	2.007
r_chiral_restr	0.065
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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	3236
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing