Experiment: 3L13

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E8X	PDB ENTRY 1E8X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	PEG 3350, 0.2M NH4SO4, 0.1M Tris-HCl 8.5, vapor diffusion, hanging drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.359	α = 90
b = 67.741	β = 95.63
c = 107.151	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		CCD	ADSC QUANTUM 315		2006-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

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	3	50	99.9	0.061	14.2	3.9		21245

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	3	3.11	100		0.441		4	2133

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1E8X	3	20	20813	1064	99.87	0.233	0.23	0.275	RANDOM	40.652

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]
-1.01		2.1	3.14		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.373
r_scangle_it	2.831
r_mcangle_it	2.79
r_mcbond_it	1.778
r_scbond_it	1.763
r_angle_refined_deg	1.187
r_angle_other_deg	0.82
r_nbd_other	0.206
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.167

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.373
r_scangle_it	2.831
r_mcangle_it	2.79
r_mcbond_it	1.778
r_scbond_it	1.763
r_angle_refined_deg	1.187
r_angle_other_deg	0.82
r_nbd_other	0.206
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.167
r_symmetry_vdw_other	0.16
r_symmetry_vdw_refined	0.142
r_nbtor_other	0.118
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6812
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.