3PN4 | pdb_00003pn4

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with actinonin (crystallized in PEG-550-MME)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PN2	PDB ENTRY 3PN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG-550-MME, Zinc sulfate 25mM, 70mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.57	α = 90
b = 56.57	β = 90
c = 146.11	γ = 90

Symmetry
Space Group	P 43 21 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	ADSC QUANTUM 315r		2009-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	ESRF	ID14-4

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	1.9	50	99.7	0.059	18.95	4.4		18505	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	1.9	2.02	99.8		0.335	4.14	4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 3PN2	1.9	40	18505	974	100	0.18322	0.18184	0.19	0.20988	0.22	RANDOM	18.274

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]
0.57			0.57		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.048
r_dihedral_angle_4_deg	18.649
r_dihedral_angle_3_deg	13.38
r_dihedral_angle_1_deg	5.582
r_scangle_it	3.224
r_scbond_it	2.13
r_angle_refined_deg	1.387
r_mcangle_it	1.157
r_mcbond_it	0.785
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.227
r_xyhbond_nbd_refined	0.224
r_symmetry_metal_ion_refined	0.221
r_nbd_refined	0.217
r_metal_ion_refined	0.196
r_symmetry_vdw_refined	0.186
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
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	1401
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	32

Software

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