8ACM | pdb_00008acm

Crystal structure of WT p38alpha

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.1,M HEPES pH 7.5, 25,%w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.32	α = 90
b = 75.16	β = 90
c = 78.67	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	Eliptically bent mirror	2020-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	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	2.14	78.67	94.3	0.085	10.6	5.5		20793			32.7

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	2.14	2.26	93.9		0.38	3.2	5.3

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	2.14	54.345	20571	1053	93.556	0.203	0.2011	0.21	0.2441	0.25	0	45.846

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]
-0.586			-1.654		2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.896
r_dihedral_angle_4_deg	21.056
r_dihedral_angle_3_deg	15.261
r_lrange_it	7.821
r_lrange_other	7.784
r_dihedral_angle_1_deg	6.368
r_scangle_it	5.071
r_scangle_other	5.07
r_mcangle_it	4.554
r_mcangle_other	4.553
r_scbond_it	3.12
r_scbond_other	3.119
r_mcbond_other	2.932
r_mcbond_it	2.931
r_angle_refined_deg	1.294
r_angle_other_deg	1.144
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.193
r_symmetry_nbd_refined	0.177
r_nbd_other	0.175
r_symmetry_xyhbond_nbd_refined	0.171
r_symmetry_nbd_other	0.169
r_nbtor_refined	0.158
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2724
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	30

Software

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