4W9K | pdb_00004w9k

pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VCB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	291	PEG 3350, MgOAc, Sodium cacodylate, DTT

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.696	α = 90
b = 93.696	β = 90
c = 361.74	γ = 90

Symmetry
Space Group	P 41 2 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	CCD	MARMOSAIC 225 mm CCD		2014-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9537	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	0.988	93.696	96.4	0.066	0.077	0.027	14.9	7.2	91790	91790

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	82.1		0.668	0.668	0.407	1.2	4.2	11112

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	1VCB	2.1	93.696	87047	4637	96.2	0.2171	0.2148	0.22	0.2596	0.26	RANDOM	50.787

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]
0.64			0.64		-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.75
r_dihedral_angle_4_deg	19.115
r_dihedral_angle_3_deg	13.535
r_dihedral_angle_1_deg	6.123
r_mcangle_it	3.246
r_mcbond_it	2.034
r_mcbond_other	2.034
r_angle_refined_deg	1.283
r_angle_other_deg	0.759
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.75
r_dihedral_angle_4_deg	19.115
r_dihedral_angle_3_deg	13.535
r_dihedral_angle_1_deg	6.123
r_mcangle_it	3.246
r_mcbond_it	2.034
r_mcbond_other	2.034
r_angle_refined_deg	1.283
r_angle_other_deg	0.759
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10493
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	176

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
XSCALE	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.