4ZWE | pdb_00004zwe

Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant

X-RAY DIFFRACTION

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	BATCH MODE	7.4	298	SPG buffer, PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.083	α = 90
b = 146.091	β = 115.03
c = 98.463	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	PSI PILATUS 6M		2015-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9792	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.8	50	98.7	0.194	0.199	0.099	3.2	6.9		54764

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	99.7		0.736	0.333		7.1	2744

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	2.81	50	51938	2789	98.07	0.2101	0.208	0.21	0.2477	0.25	RANDOM	70.01

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]
0.08		1.59	-1.21		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.082
r_dihedral_angle_3_deg	20.365
r_dihedral_angle_4_deg	19.261
r_mcangle_it	4.93
r_dihedral_angle_1_deg	4.907
r_mcbond_it	3.134
r_mcbond_other	3.133
r_angle_refined_deg	1.487
r_angle_other_deg	1.425
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.082
r_dihedral_angle_3_deg	20.365
r_dihedral_angle_4_deg	19.261
r_mcangle_it	4.93
r_dihedral_angle_1_deg	4.907
r_mcbond_it	3.134
r_mcbond_other	3.133
r_angle_refined_deg	1.487
r_angle_other_deg	1.425
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15700
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	377

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.