3KHF | pdb_00003khf

The crystal structure of the PDZ domain of human Microtubule Associated Serine/Threonine Kinase 3 (MAST3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V90	2V90, 2VPH, 2Z17
experimental model	PDB	2VPH	2V90, 2VPH, 2Z17
experimental model	PDB	2Z17	2V90, 2VPH, 2Z17

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	0.2 M Lithium Sulphate; 0.1 M Tris pH 9; 35% PEG4K, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.65	α = 90
b = 55.537	β = 90
c = 59.387	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	MARMOSAIC 225 mm CCD		2008-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00001	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.2	36.59	99.7	0.087	0.087	14.1	7.1	50856	50856			11.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.2	1.26	99.2		0.292	0.292	5.4	6.5	46964

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 (All)	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	2V90, 2VPH, 2Z17	1.2	36.59	48172	48172	2616	99.57	0.1572	0.1572	0.15646	0.16	0.1708	0.18	RANDOM	10.112

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]
-0.08			-0.02		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.568
r_dihedral_angle_4_deg	17.554
r_dihedral_angle_3_deg	13.89
r_sphericity_free	5.994
r_dihedral_angle_1_deg	5.972
r_scangle_it	3.975
r_sphericity_bonded	3.425
r_scbond_it	2.704
r_mcangle_it	2.239
r_angle_refined_deg	1.444
r_mcbond_it	1.396
r_rigid_bond_restr	1.206
r_angle_other_deg	0.893
r_mcbond_other	0.597
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1549
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling