2I7D | pdb_00002i7d

Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	50mM KH2PO4, 2-15% w/v PEG 8000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.623	α = 68.92
b = 47.153	β = 81.69
c = 62.384	γ = 74.99

Symmetry
Space Group	P 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	CCD	MAR CCD 165 mm		2003-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8133	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.2	19.12	93.1	0.067	0.068	10.24	3.5	120303	120303			13.959

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.2	1.3	86.8		0.357	0.31	3.2		23589

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.2	19.1	118444	118444	6001	94.67	0.167	0.166	0.166	0.17	0.196	0.2	RANDOM	13.221

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]
			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.468
r_dihedral_angle_4_deg	16.413
r_dihedral_angle_3_deg	12.365
r_dihedral_angle_1_deg	5.649
r_scangle_it	3.174
r_sphericity_free	3.128
r_sphericity_bonded	2.553
r_scbond_it	2.538
r_rigid_bond_restr	1.914
r_mcangle_it	1.614
r_angle_refined_deg	1.463
r_mcbond_it	1.148
r_nbtor_refined	0.292
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.096
r_symmetry_hbond_refined	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3173
Nucleic Acid Atoms
Solvent Atoms	692
Heterogen Atoms	44

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
CNS	phasing