3I5Z | pdb_00003i5z

Crystal structure of ERK2 bound to (S)-N-(2-hydroxy-1-phenylethyl)-4-(5-methyl-2-(phenylamino)pyrimidin-4-yl)-1H-pyrrole-2-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in-house unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	Protein: 14 mg/ml, 20 mM Tris-HCl pH 7.0, 5 mM DTT, 200 mM NaCl. Precipitant: 100 mM HEPES pH 7.2, 28-30% PEG MME 2000, 200 mM Ammonium sulfate, 20 mM 2-Mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.948	α = 90
b = 70.751	β = 90
c = 118.46	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	IMAGE PLATE	RIGAKU RAXIS	Yale mirrors	2001-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.2	91	95.2	0.073	12.3			18555

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	2.2	2.26	75.4		0.301			1185

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	in-house unpublished structure	2.2	60.74	18112	1424	93	0.217	0.214	0.2121	0.258	0.2521	RANDOM	20.622

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]
-0.52			-1.04		1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.888
r_dihedral_angle_4_deg	16.931
r_dihedral_angle_3_deg	16.754
r_dihedral_angle_1_deg	5.071
r_scangle_it	1.975
r_scbond_it	1.205
r_angle_refined_deg	1.156
r_mcangle_it	0.843
r_mcbond_it	0.448
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2694
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	51

Software

Software
Software Name	Purpose
d*TREK	data scaling
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing