3KC3 | pdb_00003kc3

MK2 complexed to inhibitor N4-(7-(benzofuran-2-yl)-1H-indazol-5-yl)pyrimidine-2,4-diamine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	1.75 M Ammonium Sulfate, 0.1 M Na Citrate, pH 8.0., VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.351	α = 90
b = 179.793	β = 90
c = 214.376	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	CCD	ADSC QUANTUM 210		2005-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.9	50		0.093	27	5.6		116686

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3			0.401	3.83	2.6	10342

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	2.9	20	110192	5825	97.35	0.23324	0.22987	0.22	0.29759	0.29	RANDOM	66.829

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]
0.07			-0.05		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.767
r_dihedral_angle_3_deg	22.769
r_dihedral_angle_4_deg	21.867
r_dihedral_angle_1_deg	7.387
r_scangle_it	3.596
r_scbond_it	2.169
r_angle_refined_deg	1.928
r_mcangle_it	1.808
r_mcbond_it	1.035
r_symmetry_hbond_refined	0.394

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.767
r_dihedral_angle_3_deg	22.769
r_dihedral_angle_4_deg	21.867
r_dihedral_angle_1_deg	7.387
r_scangle_it	3.596
r_scbond_it	2.169
r_angle_refined_deg	1.928
r_mcangle_it	1.808
r_mcbond_it	1.035
r_symmetry_hbond_refined	0.394
r_symmetry_vdw_refined	0.368
r_nbtor_refined	0.328
r_nbd_refined	0.265
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27853
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	286

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.