4QTA | pdb_00004qta

Structure of human ERK2 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket

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	7.5	277.15	30% PEG4000 and 0.2 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.82	α = 90
b = 75.54	β = 90
c = 103.59	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	PSI PILATUS 6M	Kirkpatrick Baez bimorph mirror pair	2013-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97960	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	1.45	33	99.9	0.09	12.5	7.9	60441	60366			11.9

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	1.45	1.53	99.7		0.71	2.6	7.5	8701

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	1.45	61.04	2	60366	57320	3046	99.93	0.16008	0.15839	0.16	0.19147	0.19	RANDOM	21.194

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]
-0.69			0.09		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.044
r_dihedral_angle_4_deg	18.069
r_dihedral_angle_3_deg	11.93
r_long_range_B_other	6.889
r_long_range_B_refined	6.887
r_dihedral_angle_1_deg	5.318
r_scangle_other	2.745
r_scbond_it	1.8
r_scbond_other	1.8
r_angle_refined_deg	1.698
r_mcangle_it	1.592
r_mcangle_other	1.592
r_mcbond_it	0.994
r_mcbond_other	0.993
r_angle_other_deg	0.853
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2715
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	86

Software

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