Experiment: 1IYB

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291.15	ammonium dihydrogen, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.8	α = 90
b = 94.3	β = 90
c = 98.1	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	CCD	OXFORD PX210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	1.5	37.43	93.2	0.052	28.6	5.6		62367	1	1	14.6

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)
	1.5	1.55	53.8		0.201	2.7	1.7	3581

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DIX	1.5	37.41	62367	62367	3152	92.5	0.212	0.23	RANDOM	13

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]
0.61			-1.08		0.48

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.4
c_scangle_it	2.77
c_scbond_it	1.91
c_mcangle_it	1.49
c_angle_deg	1.4
c_mcbond_it	1.01
c_improper_angle_d	0.89
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3258
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	48

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
CNS	refinement
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.