7Z6I | pdb_00007z6i

Crystal structure of p38alpha C162S in complex with SB20358 and CAS 2094667-81-7 (behind catalytic site; Y35 in), P 21 21 21

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	293	0.087 M Ca Acetate 0.1M MES pH 6.0 7.1% PEG 550MME

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.142	α = 90
b = 74.57	β = 90
c = 77.55	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	100	PIXEL	DECTRIS PILATUS 6M	Elliptically bent mirror	2020-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	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	2.25	77.55	100	0.092	16.5	5.6		18525			28.9

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	2.25	2.37	100		0.451	9.2	5.6

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4LOO	2.25	53.752	18480	884	99.957	0.195	0.1929	0.2	0.2479	0.25	random	36.604

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]
-0.918			-1.492		2.409

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.399
r_dihedral_angle_6_deg	13.867
r_lrange_it	6.405
r_lrange_other	6.329
r_dihedral_angle_1_deg	5.721
r_dihedral_angle_2_deg	4.757
r_scangle_it	3.968
r_scangle_other	3.967
r_mcangle_it	3.813
r_mcangle_other	3.812
r_scbond_it	2.304
r_scbond_other	2.304
r_mcbond_it	2.257
r_mcbond_other	2.255
r_angle_refined_deg	1.182
r_angle_other_deg	0.409
r_nbd_refined	0.214
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.18
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.146
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.05
r_chiral_restr	0.048
r_gen_planes_refined	0.004
r_bond_refined_d	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	2824
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	50

Software

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