3RP9 | pdb_00003rp9

Crystal Structure of the apo MapK from Toxoplasma Gondii, 25.m01780 or TGME49_007820

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NIE	PDB ENTRY 3NIE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	25% PEG3350, 0.1 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 10 mM magnesium chloride, 10 mM TCEP, cryoprotectant: 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.508	α = 90
b = 97.454	β = 104.92
c = 48.374	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	ADSC QUANTUM 315		2011-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	2.35	33.732	100	0.055	12.9	3.7	33792	17378			49.9

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	2.35	2.39	100		0.55	2.41	3.2	879

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 3NIE	2.4	33.732	16332	16264	823	99.58	0.2031	0.2012	0.2	0.2375	0.24	RANDOM	48.039

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]
0.3		-0.88	1.51		-2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.52
r_dihedral_angle_3_deg	15.347
r_dihedral_angle_4_deg	14.657
r_dihedral_angle_1_deg	5.271
r_scangle_it	2.266
r_scbond_it	1.427
r_angle_refined_deg	1.223
r_mcangle_it	0.918
r_angle_other_deg	0.86
r_mcbond_it	0.486

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.52
r_dihedral_angle_3_deg	15.347
r_dihedral_angle_4_deg	14.657
r_dihedral_angle_1_deg	5.271
r_scangle_it	2.266
r_scbond_it	1.427
r_angle_refined_deg	1.223
r_mcangle_it	0.918
r_angle_other_deg	0.86
r_mcbond_it	0.486
r_mcbond_other	0.101
r_chiral_restr	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2827
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.