1XJE

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R1R	pdb entry 1R1R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	PEG8000, sodium acetate, sodium chloride, dithiotreithol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.391	α = 90
b = 124.376	β = 103.68
c = 107.243	γ = 90

Symmetry
Space Group	C 1 2 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	MARRESEARCH		2002-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.811	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	18	97.2	0.07	12.23	2.7		119507

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	96.6		0.399	3.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1R1R	1.9	18	110169	5794	97.16	0.18445	0.18241	0.22268	RANDOM	31.972

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]
1.96		1.3	0.4		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.73
r_dihedral_angle_4_deg	19.657
r_dihedral_angle_3_deg	16.342
r_dihedral_angle_1_deg	6.898
r_scangle_it	3.66
r_scbond_it	2.633
r_angle_refined_deg	1.78
r_mcangle_it	1.595
r_mcbond_it	1.375
r_angle_other_deg	0.948
r_symmetry_vdw_other	0.337
r_symmetry_vdw_refined	0.275
r_mcbond_other	0.267
r_nbd_refined	0.221
r_nbd_other	0.187
r_symmetry_hbond_refined	0.185
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.165
r_metal_ion_refined	0.133
r_chiral_restr	0.125
r_nbtor_other	0.089
r_bond_refined_d	0.019
r_xyhbond_nbd_other	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10001
Nucleic Acid Atoms
Solvent Atoms	791
Heterogen Atoms	122

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling