3S8C | pdb_00003s8c

Structure of Yeast Ribonucleotide Reductase 1 R293A with AMPPNP and CDP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7	298	20-25% PEG 3350, 0.1 M HEPES, 0.1 M sodium chloride, pH 7.0, EVAPORATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.781	α = 90
b = 116.81	β = 90
c = 64.126	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		CCD	ADSC QUANTUM 315		2011-03-26	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.77	40.29	98.33	0.14	15.2	7.2	20834	18704

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.77	2.85	99.6		0.58	2.2	7.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Isomorphous	THROUGHOUT	2.77	40.29	20834	18704	2086	98.33	0.20236	0.19627	0.2	0.25588	0.26	RANDOM	56.958

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]
-2.79			-2.89		5.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.781
r_dihedral_angle_3_deg	19.38
r_dihedral_angle_4_deg	18.415
r_dihedral_angle_1_deg	6.773
r_scangle_it	3.182
r_scbond_it	2.018
r_angle_refined_deg	1.748
r_mcangle_it	1.431
r_mcbond_it	0.804
r_nbtor_refined	0.321
r_metal_ion_refined	0.26
r_nbd_refined	0.223
r_symmetry_vdw_refined	0.21
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.117
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
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	5254
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	57

Software

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