3PN3

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with inhibitor 21

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	17% PEG-3350, Zinc acetate 200mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.6	α = 90
b = 55.61	β = 90
c = 149.53	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 315		2007-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.970	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	50	98.5	0.066	19.33	8	114769	113073	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.38	96.9		0.398	5.13	8.1	18312

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	rigid body	THROUGHOUT	PDB entry 3M6O	1.3	44.62	107411	5659	98.57	0.15996	0.15945	0.16948	RANDOM	13.993

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]
-0.08			-0.07		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.871
r_dihedral_angle_4_deg	15.25
r_dihedral_angle_3_deg	10.656
r_dihedral_angle_1_deg	5.359
r_scangle_it	2.056
r_scbond_it	1.341
r_angle_refined_deg	1.143
r_mcangle_it	0.792
r_mcbond_it	0.471
r_nbtor_refined	0.305
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.122
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.074
r_metal_ion_refined	0.074
r_symmetry_metal_ion_refined	0.032
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2832
Nucleic Acid Atoms
Solvent Atoms	611
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
XDS	data reduction
XDS	data scaling
CNS	phasing