Experiment: 3ICT

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	288	8-16% PEG 8000, 2% 2-methyl-2,4-pentanediol, 0.2M potassium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.62	α = 90
b = 110.55	β = 101.84
c = 80.08	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	CCD	ADSC QUANTUM 4			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	0.9799	NSLS	X26C

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	2.1	46.13	99.8	0.09	0.077		132382

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	2.1	2.154	100		0.414	2.6		132117

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	3ICR	2.1	46.13	63667	3390	99.85	0.21534	0.21321	0.25498	RANDOM	47.365

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]
0.3		-0.01	-0.27		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.491
r_dihedral_angle_4_deg	20.633
r_dihedral_angle_3_deg	14.405
r_dihedral_angle_1_deg	4.948
r_scangle_it	4.315
r_scbond_it	2.769
r_mcangle_it	1.742
r_mcbond_it	1.395
r_angle_refined_deg	1.389
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.491
r_dihedral_angle_4_deg	20.633
r_dihedral_angle_3_deg	14.405
r_dihedral_angle_1_deg	4.948
r_scangle_it	4.315
r_scbond_it	2.769
r_mcangle_it	1.742
r_mcbond_it	1.395
r_angle_refined_deg	1.389
r_nbtor_refined	0.31
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.198
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8600
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	229

Software

Software
Software Name	Purpose
CBASS	data collection
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
REFMAC	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.