2CJS | pdb_00002cjs

Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	VAPOR DIFFUSION; HANGING DROP; PROTEIN: 10 MG/ML MUNC13-1/RIM2ALPHA IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4); RESERVOIR: 0.3 M AMMONIUM TARTRATE (PH 7.0); DROP: 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR; TEMPERATURE: 20 DEGREES CELSIUS; CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF ABOUT 0.06 MM X 0.06 MM X 0.25 MM WITHIN 4 DAYS.

Crystal Properties
Matthews coefficient	Solvent content
3	59.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.248	α = 90
b = 93.534	β = 90
c = 113.128	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 CCD		2005-02-12	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	1.78	37.57	99.7	0.06	36.1	5		51718		-3

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	1.78	1.81	99.6		0.7	2.8	4.8

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	1.78	50	50187	1593	99.7	0.176	0.175	0.17	0.219	0.22	RANDOM	30.79

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]
-1.38			0.82		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.18
r_dihedral_angle_4_deg	16.535
r_dihedral_angle_3_deg	14.488
r_dihedral_angle_1_deg	6.528
r_scangle_it	4.431
r_scbond_it	2.893
r_mcangle_it	1.982
r_angle_refined_deg	1.752
r_mcbond_it	1.339
r_nbtor_refined	0.31
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.206
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.133
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
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_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2949
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	58

Software

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