7Z9T | pdb_00007z9t

Crystal structure of p38alpha C162S in complex with ATPgS and CAS 2094667-81-7 (in catalytic site, Y35 out), P 1 21 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LOO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	293	27.5% PEG3350, 0.1M BIS-TRIS pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.141	α = 90
b = 68.072	β = 94.78
c = 79.98	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M	Elliptically bent mirror	2020-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

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	2.6	79.7	99.2	0.086	9.2	3		22113			43.8

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	2.6	2.74	99		0.465	3.5	3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4LOO	2.6	79.7	22092	1103	98.89	0.202	0.1994	0.2	0.2541	0.26	56.94

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]
-0.442		1.034	-1.953		2.192

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.218
r_dihedral_angle_6_deg	12.707
r_lrange_it	7.357
r_lrange_other	7.35
r_dihedral_angle_2_deg	6.227
r_dihedral_angle_1_deg	6.159
r_mcangle_it	4.304
r_mcangle_other	4.303
r_scangle_it	3.961
r_scangle_other	3.96
r_mcbond_it	2.432
r_mcbond_other	2.432
r_scbond_it	2.224
r_scbond_other	2.224
r_angle_refined_deg	1.056
r_angle_other_deg	0.352
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.205
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.178
r_nbd_other	0.175
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.045
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5641
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing