1PIU | pdb_00001piu

OXIDIZED RIBONUCLEOTIDE REDUCTASE R2-D84E MUTANT CONTAINING OXO-BRIDGED DIFERRIC CLUSTER

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RIB	Oxidized wildtype ribonucleotide reductase R2 without metal ions or solvent molecules

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	310	20% PEG 4000, 200mM NaCl, 50mM MES, 0.3% dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.1	α = 90
b = 84.6	β = 90
c = 114.8	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		1998-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.08	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	25	98.8			37295	36848			16

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.34	99.2

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Oxidized wildtype ribonucleotide reductase R2 without metal ions or solvent molecules	2.2	20.75	36848	36848	1845	98.9	0.195	0.191	0.191	0.232	RANDOM	26

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]
-4.95			2.03		2.92

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.9
c_scangle_it	4.29
c_scbond_it	3.03
c_mcangle_it	2.51
c_mcbond_it	1.71
c_angle_deg	1.1
c_improper_angle_d	0.76
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5570
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	16

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.