4QTE | pdb_00004qte

Structure of ERK2 in complex with VTX-11e, 4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYLPYRIMIDIN-4-YL}-N-[(1S)-1-(3-CHLOROPHENYL)-2-HYDROXYETHYL]-1H-PYRROLE-2-CARBOXAMIDE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ERK	pdb entry 1ERK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277.15	25% PEG smears (PEG2000, PEG3350, PEG4000 and PEG5000MME), 0.1 M cacodylate pH 5.5 and 0.2 M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.729	α = 90
b = 96.729	β = 90
c = 95.382	γ = 120

Symmetry
Space Group	P 32 2 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	PSI PILATUS 6M	Kirkpatrick Baez bimorph mirror pair	2014-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

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	1.5	21.57	98.2	0.064	15.3	7.1	81004	81001			17.9

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	1.5	1.58	96.9		0.652	3	7.1	11574

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	pdb entry 1ERK	1.5	83.77	2	81001	77002	3995	97.91	0.14667	0.1456	0.15	0.16709	0.17	RANDOM	33.32

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]
0.33	0.17		0.33		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.766
r_dihedral_angle_4_deg	17.655
r_dihedral_angle_3_deg	11.96
r_long_range_B_other	7.74
r_long_range_B_refined	7.738
r_dihedral_angle_1_deg	5.967
r_scangle_other	2.886
r_scbond_it	2.177
r_scbond_other	2.176
r_angle_refined_deg	1.617
r_mcangle_it	1.562
r_mcangle_other	1.562
r_mcbond_it	1.037
r_mcbond_other	1.036
r_angle_other_deg	0.823
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2846
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms	149

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling