2H4J | pdb_00002h4j

Sir2-deacetylated peptide (from enzymatic turnover in crystal)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YC5	PDB Entry: 1yc5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.6	293	CHES, PEG3350, PH9.6, acetylated peptide. Crystals were soaked in cryo + 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.049	α = 90
b = 59.683	β = 90
c = 107.35	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		2005-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

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	2.1	50	99.9	0.092	20.3	6.9	17933	16973	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB Entry: 1yc5	2.1	50	2	16886	16973	913	99.94	0.19999	0.19762	0.2	0.24619	0.25	RANDOM	30.982

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]
0.39			0.08		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.645
r_dihedral_angle_4_deg	19.404
r_dihedral_angle_3_deg	13.714
r_sphericity_free	7.971
r_dihedral_angle_1_deg	6.467
r_scangle_it	4.765
r_rigid_bond_restr	4.503
r_scbond_it	4.39
r_sphericity_bonded	3.349
r_mcangle_it	2.394
r_angle_refined_deg	1.744
r_mcbond_it	1.612
r_nbtor_refined	0.302
r_nbd_refined	0.227
r_symmetry_hbond_refined	0.16
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.11
r_bond_refined_d	0.019
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1936
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	phasing