4DJN

Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from Homo sapiens at 2.20 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	2.0M ammonium sulfate, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.053	α = 90
b = 98.762	β = 90
c = 133.668	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	PIXEL	DECTRIS PILATUS 6M	Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator	2011-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

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	2.2	29.834	97.5	0.105	9.8	6.3	45830	45830

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)
1	2.2	2.26	95.8		0.73	0.73	1.7	3.9	3169

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.2	29.834	45754	2320	97.14	0.1945	0.1931	0.2191	RANDOM	56.1845

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]
1.07			0.88		-1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.007
r_dihedral_angle_4_deg	15.375
r_dihedral_angle_3_deg	14.822
r_dihedral_angle_1_deg	4.95
r_angle_refined_deg	1.173
r_angle_other_deg	1.108
r_nbd_refined	0.216
r_nbd_other	0.21
r_symmetry_vdw_refined	0.2
r_symmetry_vdw_other	0.188

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.007
r_dihedral_angle_4_deg	15.375
r_dihedral_angle_3_deg	14.822
r_dihedral_angle_1_deg	4.95
r_angle_refined_deg	1.173
r_angle_other_deg	1.108
r_nbd_refined	0.216
r_nbd_other	0.21
r_symmetry_vdw_refined	0.2
r_symmetry_vdw_other	0.188
r_nbtor_refined	0.187
r_nbtor_other	0.104
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4674
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	13

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.