8PAS | pdb_00008pas

Crystal structure of MAP4K1 with a SMOL inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other		PREVIOUSLY SOLVED STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	NOT DISCLOSED

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.04	α = 90
b = 100.056	β = 102.03
c = 61.055	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		2017-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99998	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	CC (Half)	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	2.7	42.91	96.1	0.041	0.049	0.999	21.55	3		19051

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.95	97		0.439	0.529	0.936	3.5	3.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	42.91	18239	811	96.42	0.23093	0.22808	0.23	0.2997	0.3	RANDOM	81.876

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]
1.03		1.35	-4.57		2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.029
r_dihedral_angle_4_deg	22.373
r_dihedral_angle_3_deg	19.622
r_dihedral_angle_1_deg	8.373
r_long_range_B_refined	6.885
r_long_range_B_other	6.884
r_mcangle_it	4.687
r_mcangle_other	4.687
r_scangle_other	4.682
r_mcbond_it	2.898
r_mcbond_other	2.898
r_scbond_it	2.853
r_scbond_other	2.852
r_angle_refined_deg	1.887
r_angle_other_deg	1.382
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4282
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building
PHASER	phasing