8ZAD | pdb_00008zad

Crystal structure of RuABA3 from Rutstroemia sp. NJR-2017a WRK4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG 8000, 0.1 M CAPS pH 10.5, 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.324	α = 90
b = 141.011	β = 90
c = 90.285	γ = 90

Symmetry
Space Group	C 2 2 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	Bruker PHOTON III		2021-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

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	2.1	36.39	99.9	0.996	8.5	7.62		25866

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	2.1	2.13			0.792

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	AlphaFold	2.1	36.39	24504	1308	99.87	0.16631	0.16388	0.1743	0.21166	0.2196	RANDOM	23.186

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]
0.76			-1.13		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.685
r_dihedral_angle_4_deg	20.239
r_dihedral_angle_3_deg	15.156
r_dihedral_angle_1_deg	6.128
r_long_range_B_refined	5.919
r_long_range_B_other	5.749
r_scangle_other	4.211
r_mcangle_other	3.008
r_mcangle_it	3.006
r_scbond_it	2.676
r_scbond_other	2.675
r_mcbond_it	1.949
r_mcbond_other	1.944
r_angle_refined_deg	1.6
r_angle_other_deg	1.425
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2798
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
SAINT	data reduction
PHASER	phasing