6Z3C

High resolution structure of RgNanOx

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Z3B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG3000, sodium citrate,

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.11	α = 90
b = 54.97	β = 90
c = 282.43	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	80	PIXEL	DECTRIS PILATUS3 6M		2019-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

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	1.74	47.47	100	1	5.6	6.3		93221

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	1.74	1.77			0.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6Z3B	1.74	47.47	78180	3831	99.819	0.184	0.1821	0.2226	17.448

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]
0.996			-0.985		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.245
r_dihedral_angle_4_deg	23.814
r_dihedral_angle_3_deg	12.866
r_lrange_it	9.087
r_lrange_other	9.062
r_scangle_it	8.278
r_scangle_other	8.277
r_dihedral_angle_1_deg	7.074
r_scbond_other	6.817
r_scbond_it	6.816
r_mcangle_it	3.782
r_mcangle_other	3.775
r_mcbond_it	3.165
r_mcbond_other	3.156
r_angle_refined_deg	1.517
r_angle_other_deg	1.473
r_symmetry_nbd_refined	0.409
r_nbd_other	0.303
r_symmetry_xyhbond_nbd_other	0.227
r_nbd_refined	0.214
r_symmetry_nbd_other	0.18
r_xyhbond_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.167
r_ncsr_local_group_1	0.101
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5919
Nucleic Acid Atoms
Solvent Atoms	850
Heterogen Atoms	114

Software

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