7Q3C | pdb_00007q3c

Ribonucleotide Reductase AaR2 protein from Aquifex aeolicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AIL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M citrate pH 4.0, 1.0 M lithium chloride, 20 % PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.183	α = 90
b = 69.183	β = 90
c = 177.5	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS EIGER2 X 16M		2021-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.15	48.968	100	1	24.6	25.1		24392

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.22			0.69

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7AIL	2.15	48.968	24313	1203	99.975	0.25	0.2471	0.25	0.3145	0.32	61.901

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]
1.08			1.08		-2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.617
r_dihedral_angle_4_deg	19.513
r_dihedral_angle_3_deg	16.717
r_lrange_it	6.996
r_lrange_other	6.924
r_dihedral_angle_1_deg	5.752
r_mcangle_it	4.602
r_mcangle_other	4.601
r_scangle_it	4.557
r_scangle_other	4.556
r_mcbond_it	3.072
r_mcbond_other	3.069
r_scbond_it	2.868
r_scbond_other	2.867
r_angle_refined_deg	1.194
r_angle_other_deg	1.118
r_nbd_refined	0.19
r_symmetry_nbd_refined	0.186
r_nbd_other	0.181
r_symmetry_nbd_other	0.17
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_other	0.077
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.05
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	2667
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing