3TB9 | pdb_00003tb9

Structure of Yeast Ribonucleotide Reductase 1 Q288A with AMPPNP and CDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CVU	PDB ENTRY 2CVU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.1M HEPES pH 7.0, 15-25% PEG 3350, 0.2M NaCl, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.886	α = 90
b = 116.959	β = 90
c = 64.329	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	CCD	ADSC QUANTUM 315		2011-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.98	APS	24-ID-E

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	2.53	50	100	0.105	25	7.9	28484	28484

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	2.53	2.59	100		0.519	5	8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2CVU	2.53	43.48	28484	25067	2793	99.9	0.20248	0.19853	0.2	0.2375	0.24	RANDOM	39.857

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]
-1.49			-2.05		3.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.645
r_dihedral_angle_4_deg	19.033
r_dihedral_angle_3_deg	18.243
r_dihedral_angle_1_deg	6.219
r_scangle_it	3.08
r_scbond_it	1.944
r_angle_refined_deg	1.468
r_mcangle_it	1.397
r_mcbond_it	0.75
r_nbtor_refined	0.307
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.163
r_symmetry_vdw_refined	0.155
r_chiral_restr	0.105
r_symmetry_hbond_refined	0.099
r_bond_refined_d	0.012
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	5107
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	57

Software

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