4DR9 | pdb_00004dr9

Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LRY	pdb deposition 1lry, modified with CCP4 program CHAINSAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	HAMPTON RESEARCH INDEX H12: 30% PEG 2000 MME, 150MM KBR, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K; 18 hour soak in reservoir solution containing 1mM actinonin

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.25	α = 80.87
b = 65.78	β = 76.82
c = 68.29	γ = 82.75

Symmetry
Space Group	P 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	2012-02-07	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT
2	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	99.6	0.077	0.077	17	5.8	56808	56579		-3	22.89

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	98		0.49	0.49	2.02	2.5	4200

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 (All)	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	pdb deposition 1lry, modified with CCP4 program CHAINSAW	1.9	50	56808	56577	2852	99.6	0.185	0.185	0.182	0.1866	0.235	0.2369	RANDOM	18.66

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]
-0.18	0.01	0.4	0.7	-0.1	-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.807
r_dihedral_angle_4_deg	13.148
r_dihedral_angle_3_deg	12.543
r_dihedral_angle_1_deg	6.033
r_angle_refined_deg	1.603
r_angle_other_deg	0.924
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
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	5570
Nucleic Acid Atoms
Solvent Atoms	564
Heterogen Atoms	117

Software

Software
Software Name	Purpose
JDirector	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling