7MMV | pdb_00007mmv

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae with Cu(I) bound (Cu sulfate soak)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EBO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	18% (w/v) PEG 3350, 0.2 M magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.735	α = 90
b = 46.743	β = 90.32
c = 133.922	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 300 mm CCD		2020-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9787	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.78	50	98	0.147	0.158	0.058	6.7	7.3		62957

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	96.7		0.957	1.038	0.4	0.825		6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	6EBO	1.78	38.36	59842	3053	97.89	0.1815	0.1801	0.1898	0.2086	0.2218	RANDOM	19.261

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]
0.22		0.1	-0.05		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.003
r_dihedral_angle_3_deg	13.434
r_dihedral_angle_4_deg	9.238
r_dihedral_angle_1_deg	5.401
r_angle_other_deg	1.221
r_angle_refined_deg	1.156
r_chiral_restr	0.058
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5065
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	18

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction