5Y3A | pdb_00005y3a

Crystal structure of Ragulator complex (p18 49-161)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MS6	3MS6, 1VET
experimental model	PDB	1VET	3MS6, 1VET

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	289	0.1 M Bis-Tris (pH 5.5), and 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.341	α = 90
b = 89.626	β = 90
c = 232.173	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	RAYONIX MX225HE		2015-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.9793	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50.01	90	0.105	0.12	0.056	10.1	4.1		30426

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	88.4		0.54	0.616	0.291	0.841		4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3MS6, 1VET	2.9	50.01	27052	1457	84.34	0.24788	0.24563	0.25	0.28849	0.29	RANDOM	42.125

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]
-5.1			0.72		4.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.395
r_sphericity_bonded	23.596
r_dihedral_angle_3_deg	19.011
r_dihedral_angle_4_deg	15.343
r_dihedral_angle_1_deg	5.557
r_long_range_B_refined	2.118
r_rigid_bond_restr	1.732
r_scbond_it	1.551
r_angle_refined_deg	1.336
r_mcangle_it	1.307
r_mcbond_it	1.176
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
r_long_range_B_other
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7411
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing