2CVS | pdb_00002cvs

Structures of Yeast Ribonucleotide Reductase I

X-RAY DIFFRACTION

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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 = 109.511	α = 90
b = 117.166	β = 90
c = 63.362	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		2004-06-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418, 0.91900, 0.91940

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	2.6	50	97.6	0.072	0.072	20.1	3.3	23818	23818

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)
	2.6	2.69	98.9		0.445	0.445	2.4	3.1	3098

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	MAD	THROUGHOUT	2.6	50	22679	2547	97.76	0.21071	0.20436	0.2	0.26693	0.27	RANDOM	51.692

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]
-0.12			-3.09		3.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.521
r_dihedral_angle_3_deg	19.012
r_dihedral_angle_4_deg	15.267
r_dihedral_angle_1_deg	6.148
r_scangle_it	2.546
r_scbond_it	1.598
r_angle_refined_deg	1.47
r_mcangle_it	1.419
r_mcbond_it	0.791
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.272
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.105
r_symmetry_hbond_refined	0.105
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_refined
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	5254
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms

Software

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