4BX9

Human Vps33A in complex with a fragment of human Vps16

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BX8	PDB ENTRY 4BX8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	CRYSTALS WERE GROWN IN SITTING DROPS AT 20C. VPS33A:VPS16 COMPLEX (200 NL; A280 = 7.13, APPROX. 8.7 MG/ML) WAS MIXED 1:1 WITH RESERVOIR SOLUTION AND EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 4% TACSIMATE PH 6.0, 12% PEG 3350 (HAMPTON RESEARCH). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN RESERVOIR SOLUTION SUPPLEMENTED WITH 30% ETHYLENE GLYCOL AND CRYO-COOLED BY PLUNGING INTO LIQUID NITROGEN.

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.41	α = 90
b = 128.41	β = 90
c = 263.36	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M	TOROIDAL	2012-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	2.6	87.8	100	0.11	16.8	15.2		68560		-3	76.138

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	2.6	2.72	100		1.31	2.1	14

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4BX8	2.6	85.84	65003	3465	99.98	0.17762	0.17594	0.21024	RANDOM	70.508

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]
-0.75			-0.75		1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.529
r_dihedral_angle_4_deg	19.91
r_dihedral_angle_3_deg	16.432
r_dihedral_angle_1_deg	6.239
r_angle_refined_deg	1.756
r_angle_other_deg	1.092
r_chiral_restr	0.094
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.005
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	9973
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing