2NYR | pdb_00002nyr

Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B4Y	PDB entry 2B4Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	300	25% PEG 3350, 200mM NaCl, 0.1M Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.2	α = 90
b = 116.205	β = 90.46
c = 55.993	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2005-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.00000

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.06	58.12	86.4			28096	28096

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.06	2.1	86.5

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 entry 2B4Y	2.06	58.12	26667	26667	1402	86.2	0.202	0.202	0.199	0.1998	0.269	0.2668	RANDOM	21.64

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]
0.2		-0.17	0.2		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.413
r_dihedral_angle_4_deg	19.211
r_dihedral_angle_3_deg	15.905
r_dihedral_angle_1_deg	5.297
r_angle_refined_deg	1.73
r_scangle_it	1.255
r_scbond_it	0.818
r_mcangle_it	0.562
r_mcbond_it	0.331
r_nbtor_refined	0.302
r_chiral_restr	0.245
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.159
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.127
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3947
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	88

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling