Experiment: 3IIY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SeMet Eed Structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.573	α = 90
b = 85.18	β = 90
c = 91.352	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.65	30	98.1	0.119	0.119	11.3	4.2	12915	12915		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.65	2.74	98.8		0.389	0.389	3.2	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SeMet Eed Structure	2.65	30	12670	12670	659	98.24	0.18418	0.18418	0.18036	0.25924	RANDOM	17.696

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]
0.14			-1.32		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.391
r_dihedral_angle_4_deg	16.19
r_dihedral_angle_3_deg	15.05
r_dihedral_angle_1_deg	6.442
r_scangle_it	1.876
r_angle_refined_deg	1.215
r_scbond_it	1.085
r_mcangle_it	0.914
r_mcbond_it	0.498
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.391
r_dihedral_angle_4_deg	16.19
r_dihedral_angle_3_deg	15.05
r_dihedral_angle_1_deg	6.442
r_scangle_it	1.876
r_angle_refined_deg	1.215
r_scbond_it	1.085
r_mcangle_it	0.914
r_mcbond_it	0.498
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.235
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.182
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3000
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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.