6GDM

Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	35.0%w/v MPEG 2000, 0.2M (NH4)2SO4, 0.1M HEPES/NaOHpH=7.2, 0.02M Mercaptoethanol

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.722	α = 90
b = 70.69	β = 109.45
c = 60.615	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	CCD	RIGAKU SATURN 944+		2013-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.91	57.156	97.7	0.051	14	2.7		30330

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.97	83.6		0.483	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.91	27.47	28055	1527	97.53	0.18515	0.18204	0.24265	RANDOM	33.486

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]
-0.93		0.02	0.84		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.082
r_dihedral_angle_4_deg	19.151
r_dihedral_angle_3_deg	14.637
r_dihedral_angle_1_deg	6.551
r_long_range_B_refined	5.585
r_long_range_B_other	5.542
r_scbond_it	2.707
r_scbond_other	2.706
r_mcbond_it	2.069
r_mcbond_other	2.057
r_angle_refined_deg	1.427
r_angle_other_deg	0.482
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other
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_mcangle_it
r_mcangle_other
r_scangle_it
r_scangle_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2826
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing