Experiment: 3ILD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3II2	PDB ENTRY 3II2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG 8000, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.757	α = 90
b = 64.757	β = 90
c = 85.743	γ = 120

Symmetry
Space Group	P 31 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	100	CCD	ADSC QUANTUM 4		2009-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93	ESRF	ID14-2

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	3.1	47	100	0.072	29.2	11.6		4047			80

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	3.1	3.27	100		0.404	6.8	12	572

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	PDB ENTRY 3II2	3.1	22	3788	227	100	0.27335	0.2711	0.29	0.30932	0.34	RANDOM	26.218

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]
2.57	1.29		2.57		-3.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.412
r_dihedral_angle_4_deg	18.175
r_dihedral_angle_3_deg	17.885
r_dihedral_angle_1_deg	7.08
r_scangle_it	1.689
r_angle_refined_deg	1.331
r_scbond_it	0.954
r_mcangle_it	0.789
r_mcbond_it	0.415
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.412
r_dihedral_angle_4_deg	18.175
r_dihedral_angle_3_deg	17.885
r_dihedral_angle_1_deg	7.08
r_scangle_it	1.689
r_angle_refined_deg	1.331
r_scbond_it	0.954
r_mcangle_it	0.789
r_mcbond_it	0.415
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1268
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
ADSC	data collection
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

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.