6DW3 | pdb_00006dw3

SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BZB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		298	100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.34	α = 90
b = 147.325	β = 114.64
c = 98.537	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	PIXEL	DECTRIS PILATUS 6M		2016-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97920	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.2	50	98.1	0.123	0.997	7	2.9		110334

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	98.2		0.252	0.8	2.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	4BZB	2.2	50	104740	5562	96.62	0.19205	0.1901	0.2	0.228	0.23	RANDOM	42.431

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]
1.05		0.11	-2.39		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.387
r_dihedral_angle_3_deg	17.41
r_dihedral_angle_4_deg	14.586
r_dihedral_angle_1_deg	6.155
r_long_range_B_refined	6.03
r_long_range_B_other	6.019
r_scangle_other	3.495
r_mcangle_it	2.531
r_mcangle_other	2.531
r_scbond_other	2.116
r_scbond_it	2.115
r_angle_refined_deg	2.03
r_mcbond_it	1.538
r_mcbond_other	1.536
r_angle_other_deg	1.118
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15690
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	372

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing