4W9G | pdb_00004w9g

pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(3-methyl-4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6)

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	48.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.487	α = 90
b = 93.487	β = 90
c = 363.891	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	PIXEL	DECTRIS PILATUS 6M-F		2014-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.7	48.9	99.9	0.158	6.9	6.5		45646

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	2.7	2.85	100		0.638	2	6.7

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	2.7	93.49	43222	2327	99.77	0.2238	0.2216	0.22	0.2638	0.26	RANDOM	45.456

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]
-0.04			-0.04		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.722
r_dihedral_angle_4_deg	14.861
r_dihedral_angle_3_deg	13.128
r_dihedral_angle_1_deg	5.544
r_mcangle_it	1.845
r_angle_refined_deg	1.046
r_mcbond_it	1.03
r_mcbond_other	1.03
r_angle_other_deg	0.735
r_chiral_restr	0.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.722
r_dihedral_angle_4_deg	14.861
r_dihedral_angle_3_deg	13.128
r_dihedral_angle_1_deg	5.544
r_mcangle_it	1.845
r_angle_refined_deg	1.046
r_mcbond_it	1.03
r_mcbond_other	1.03
r_angle_other_deg	0.735
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10508
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	116

Software

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