8XEY | pdb_00008xey

The Crystal Structure of C-terminal kinase domain of RSK2 from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O1S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Tris pH8.5, 25%PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.513	α = 90
b = 46.513	β = 90
c = 294.07	γ = 90

Symmetry
Space Group	P 41 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 PILATUS3 6M		2021-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000000	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.65	49.01	100	0.174	12.4	14.8		10370

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.78			0.994

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	2.65	45.984	10281	551	99.971	0.206	0.2016	0.21	0.2803	0.28	51.766

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]
3.143			3.143		-6.285

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.744
r_dihedral_angle_6_deg	14.353
r_lrange_other	11.347
r_lrange_it	11.343
r_dihedral_angle_1_deg	8.082
r_mcangle_it	7.938
r_mcangle_other	7.935
r_dihedral_angle_2_deg	7.837
r_scangle_it	7.45
r_scangle_other	7.448
r_mcbond_it	5.14
r_mcbond_other	5.138
r_scbond_it	4.801
r_scbond_other	4.799
r_angle_refined_deg	1.518
r_angle_other_deg	0.5
r_nbd_refined	0.225
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.198
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.18
r_nbd_other	0.174
r_symmetry_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2480
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	11

Software

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