2CVU | pdb_00002cvu

Structures of Yeast Ribonucleotide Reductase I

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		native structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	298	PEG 3350, sodium acetate, ammonium sulfate, pH 6.5, EVAPORATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	37.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.759	α = 90
b = 117.509	β = 90
c = 64.584	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2005-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2.9	50	99.7	0.127	0.127	13.6	4.6	18752	18752

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)
	2.9	3	100		0.408	0.408	2.1	4.7	2553

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	native structure	2.9	50	16829	1901	99.58	0.18331	0.17728	0.18	0.23595	0.24	RANDOM	37.403

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]
-1.5			-2.13		3.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.786
r_dihedral_angle_3_deg	20.339
r_dihedral_angle_4_deg	19.698
r_dihedral_angle_1_deg	6.862
r_scangle_it	2.466
r_angle_refined_deg	1.591
r_scbond_it	1.501
r_mcangle_it	1.25
r_mcbond_it	0.705
r_nbtor_refined	0.319
r_nbd_refined	0.236
r_symmetry_vdw_refined	0.211
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.109
r_symmetry_hbond_refined	0.073
r_metal_ion_refined	0.044
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5208
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	57

Software

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