6DWK | pdb_00006dwk

SAMHD1 Bound to Fludarabine-TP in the Catalytic Pocket

X-RAY DIFFRACTION

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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
2.29	46.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.691	α = 90
b = 146.671	β = 114.53
c = 99.131	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	2.3	50	99.5	0.158	0.983	9.3	5.7		100587

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	2.3	2.34	99.8		0.185		5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.3	50	95366	5169	96.31	0.17817	0.17631	0.18	0.21213	0.21	RANDOM	45.175

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]
2		-0.02	-1.11		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.945
r_dihedral_angle_3_deg	16.61
r_dihedral_angle_4_deg	14.507
r_long_range_B_refined	7.274
r_long_range_B_other	7.274
r_dihedral_angle_1_deg	5.662
r_scangle_other	3.978
r_mcangle_it	2.751
r_mcangle_other	2.751
r_scbond_it	2.527
r_scbond_other	2.507
r_angle_refined_deg	2.225
r_mcbond_it	1.701
r_mcbond_other	1.698
r_angle_other_deg	1.111
r_chiral_restr	0.121
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	15649
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	489

Software

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