8RXR | pdb_00008rxr

Crystal structure of VPS34 in complex with inhibitor SB02024

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LS8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	22.5 % PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 288.824	α = 90
b = 98.65	β = 92.266
c = 62.895	γ = 90

Symmetry
Space Group	C 1 2 1

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 6M	TOROIDAL MIRROR	2015-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97802	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.06	49.374	99.6	0.055	0.07	0.043	0.999	12.6	4.5		108408

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	2.06	2.13	99.3		0.9	1.164	0.73	0.53	1.4	4.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.06	49.374	108391	5315	99.481	0.184	0.1816	0.19	0.2245	0.23	47.699

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]
-0.131		-1.143	-0.735		0.953

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.943
r_dihedral_angle_3_deg	12.685
r_lrange_it	7.322
r_lrange_other	7.322
r_dihedral_angle_2_deg	6.213
r_scangle_it	5.924
r_scangle_other	5.924
r_dihedral_angle_1_deg	5.694
r_mcangle_it	3.867
r_mcangle_other	3.866
r_scbond_it	3.798
r_scbond_other	3.798
r_mcbond_it	2.731
r_mcbond_other	2.731
r_angle_refined_deg	1.315
r_angle_other_deg	0.467
r_nbd_refined	0.215
r_nbd_other	0.191
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_nbd_refined	0.121
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.065
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8728
Nucleic Acid Atoms
Solvent Atoms	590
Heterogen Atoms	105

Software

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