1Y8G | pdb_00001y8g

Catalytic and ubiqutin-associated domains of MARK2/PAR-1: Inactive double mutant with selenomethionine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		partially refined model of a similar construct obtained by combination of MR and MIR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 5000 MME, TACSIMATE, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.822	α = 90
b = 118.822	β = 90
c = 105.38	γ = 120

Symmetry
Space Group	P 61

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	MARRESEARCH		2004-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8031	EMBL/DESY, HAMBURG	X13

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	2.501	46.3	99.9	0.099	17.9	7.26	29259	29259			58.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.501	2.54	100

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	other	THROUGHOUT	partially refined model of a similar construct obtained by combination of MR and MIR	2.501	46.3	29259	29259	1514	99.97	0.20136	0.20136	0.19776	0.2	0.26834	0.27	RANDOM	43.887

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]
0.35	0.18		0.35		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.035
r_dihedral_angle_3_deg	19.696
r_dihedral_angle_4_deg	19.37
r_dihedral_angle_1_deg	6.249
r_scangle_it	3.368
r_scbond_it	2.249
r_angle_refined_deg	1.527
r_mcangle_it	1.468
r_mcbond_it	0.936
r_nbtor_refined	0.318
r_nbd_refined	0.232
r_symmetry_hbond_refined	0.187
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4913
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms

Software

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