8XOV | pdb_00008xov

The Crystal Structure of N-terminal kinase domain of human RSK-1 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z7Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MgAC2, 0.1M Nacacodylate pH6.5, 15% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.911	α = 90
b = 54.346	β = 94.075
c = 207.028	γ = 90

Symmetry
Space Group	I 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 PILATUS3 6M		2021-11-12	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	2.55	33.7	93.8	0.069	6	2.9		11642

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	2.55	2.66			0.456

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	2.55	33.7	11641	606	93.502	0.206	0.2032	0.21	0.2517	0.25	64.192

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]
-5.626		-0.381	9.58		-3.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.635
r_dihedral_angle_6_deg	16.259
r_lrange_other	12.744
r_lrange_it	12.743
r_scangle_it	9.761
r_scangle_other	9.759
r_mcangle_other	9.245
r_mcangle_it	9.24
r_dihedral_angle_2_deg	8.326
r_dihedral_angle_1_deg	8.313
r_scbond_it	6.507
r_scbond_other	6.504
r_mcbond_it	6.024
r_mcbond_other	5.993
r_angle_refined_deg	1.572
r_angle_other_deg	0.496
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.224
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.183
r_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_nbd_refined	0.161
r_symmetry_nbtor_other	0.083
r_chiral_restr_other	0.081
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2113
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	43

Software

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