6I6U | pdb_00006i6u

Circular permutant of ribosomal protein S6, adding 9aa to N terminal of P81-82, L75A mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RIS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Calcium chloride dehydrate 0.1 M Tris pH 8.0 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.91	α = 90
b = 43.92	β = 117.18
c = 70.63	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS EIGER X 16M		2018-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.97999	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.57	62.83	99.9	0.071	0.077	0.03	0.998	11.9	6.7		28101

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	1.57	1.59	100		0.943	1.022	0.39	0.772		6.8

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	1Ris	1.57	62.83	26699	1409	99.8	0.2103	0.2079	0.22	0.2563	0.27	RANDOM	33.166

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]
-0.12		-0.7	2.35		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.048
r_dihedral_angle_4_deg	17.94
r_dihedral_angle_3_deg	15.553
r_dihedral_angle_1_deg	6.285
r_angle_refined_deg	2.121
r_angle_other_deg	1.134
r_chiral_restr	0.123
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.048
r_dihedral_angle_4_deg	17.94
r_dihedral_angle_3_deg	15.553
r_dihedral_angle_1_deg	6.285
r_angle_refined_deg	2.121
r_angle_other_deg	1.134
r_chiral_restr	0.123
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1683
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.