4LTC | pdb_00004ltc

Crystal structure of yeast 20S proteasome in complex with enone carmaphycin analogue 6

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
3.71	66.83

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 135.17	�� = 90
b = 300.23	�� = 112.79
c = 144.38	�� = 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		2013-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		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	2.5		97.1	0.051	16.34			354256		-3	55.34

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	2.5	2.6	97.5		0.538	1.71

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	2.5	15	352662	17633	96.82	0.2055	0.2041	0.206	0.2325	0.2327	RANDOM	57.9261

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]
0.19		0.19	0.03		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.683
r_dihedral_angle_3_deg	14.056
r_dihedral_angle_4_deg	12.932
r_dihedral_angle_1_deg	5.339
r_mcangle_it	2.022
r_mcbond_it	1.112
r_mcbond_other	1.112
r_angle_refined_deg	0.91
r_angle_other_deg	0.695
r_chiral_restr	0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.683
r_dihedral_angle_3_deg	14.056
r_dihedral_angle_4_deg	12.932
r_dihedral_angle_1_deg	5.339
r_mcangle_it	2.022
r_mcbond_it	1.112
r_mcbond_other	1.112
r_angle_refined_deg	0.91
r_angle_other_deg	0.695
r_chiral_restr	0.066
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	49538
Nucleic Acid Atoms
Solvent Atoms	2607
Heterogen Atoms	74

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.