3U04

Crystal structure of peptide deformylase from ehrlichia chaffeensis in complex with actinonin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	290	EBS SCREEN JCSG+ A9: 15-20% PEG 3350, 200MM AMMONIUM CHLORIDE; EHCHA.01519.A.A1.PW27438 AT 14MG/ML, CRYO PROTECTED WITH AL'S OIL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.89	α = 90
b = 33.02	β = 91.17
c = 68.14	γ = 90

Symmetry
Space Group	C 1 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	RIGAKU SATURN 944+	RIGAKU VARIMAX HF	2011-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.7	41.936	97.8	0.031			20920	20709		-3	25.29

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	1.7	1.74	80.9		0.188	5.19

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3oca, native EhchA.01519.a	1.7	41.936	20709	20709	1062		0.172	0.17	0.198	RANDOM	23.09

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]
-0.78		0.23	1.67		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.18
r_dihedral_angle_4_deg	19.61
r_dihedral_angle_3_deg	12.31
r_dihedral_angle_1_deg	5.7
r_angle_refined_deg	1.555
r_angle_other_deg	0.941
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scbond_it
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	1329
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	30

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement