8UL0 | pdb_00008ul0

Structure of rsKiiro using SSX

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	8.4	295	0.2 M lithium sulfate, 0.1 M Tris-Cl, 25 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.6	α = 90
b = 74.5	β = 90
c = 78.9	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	290	PIXEL	DECTRIS EIGER X 4M		2019-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)

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	1.7	78.69	99.209	0.9696252	3.884	62.2434		1633393

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	1.7	1.761			0.1295		5.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.75	54.227	24164	1215	99.649	0.174	0.1721	0.1723	0.2074	0.2077	26.752

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]
0.526			0.065		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.975
r_dihedral_angle_4_deg	21.643
r_dihedral_angle_3_deg	13.656
r_lrange_other	9.692
r_lrange_it	9.682
r_scangle_it	7.926
r_scangle_other	7.668
r_dihedral_angle_1_deg	7.055
r_scbond_it	5.345
r_scbond_other	5.093
r_mcangle_it	5.085
r_mcangle_other	5.085
r_mcbond_it	3.374
r_mcbond_other	3.298
r_angle_other_deg	2.378
r_angle_refined_deg	1.704
r_symmetry_xyhbond_nbd_refined	0.37
r_nbd_refined	0.28
r_nbd_other	0.232
r_symmetry_nbd_other	0.23
r_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.14
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.072
r_xyhbond_nbd_other	0.054
r_bond_other_d	0.034
r_gen_planes_other	0.014
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1770
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrysalisPro	data scaling
REFMAC	phasing