4HNP | pdb_00004hnp

Crystal structure of yeast 20S proteasome in complex with vinylketone carmaphycin analogue VNK1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	297	30 mM of magnesium acetate, 100 mM of MES (pH 7.2) and 12% of MPD, vapor diffusion, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.85	α = 90
b = 301.36	β = 112.82
c = 144.46	γ = 90

Symmetry
Space Group	P 1 21 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	PSI PILATUS 6M		2012-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.8	48.42	98.2	0.096	8.76			257429		-3	56.903

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	2.8	2.9	97.8		0.485	2.56

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 (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	2.8	48.42	257418	12815	98.31	0.2048	0.2031	0.2032	0.2389	0.2373	RANDOM	65.0692

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]
2.94		-1.91	-7.77		3.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.877
r_dihedral_angle_3_deg	15.433
r_dihedral_angle_4_deg	14.034
r_dihedral_angle_1_deg	4.912
r_angle_refined_deg	0.95
r_scangle_it	0.795
r_scbond_it	0.435
r_mcangle_it	0.315
r_mcbond_it	0.162
r_chiral_restr	0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.877
r_dihedral_angle_3_deg	15.433
r_dihedral_angle_4_deg	14.034
r_dihedral_angle_1_deg	4.912
r_angle_refined_deg	0.95
r_scangle_it	0.795
r_scbond_it	0.435
r_mcangle_it	0.315
r_mcbond_it	0.162
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	49538
Nucleic Acid Atoms
Solvent Atoms	750
Heterogen Atoms	216

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CNS	phasing

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.