Experiment: 3I25

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5	299	16% PEG8000, 0.1M Citrate, 0.3M Lithium sulphate, 0.1M Sodium Chloride, pH 5.0, VAPOR DIFFUSION, temperature 299K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.417	α = 90
b = 102.483	β = 103.53
c = 100.186	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 1		2007-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.98	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	2.1	102.6	95.8	0.055	15.1	3		89314	2	2	38

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)
	2.1	2.21	79.3		0.271	4.2	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ENTRY 3DM6	2.1	79.16	2	84864	4449	95.74	0.212	0.202	0.2	0.238	RANDOM	37.954

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]
0.1		0.19	0.19		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.858
r_dihedral_angle_4_deg	18.883
r_dihedral_angle_3_deg	16.863
r_dihedral_angle_1_deg	7.934
r_scangle_it	4.24
r_scbond_it	2.81
r_mcangle_it	2.043
r_angle_refined_deg	1.886
r_mcbond_it	1.278
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.858
r_dihedral_angle_4_deg	18.883
r_dihedral_angle_3_deg	16.863
r_dihedral_angle_1_deg	7.934
r_scangle_it	4.24
r_scbond_it	2.81
r_mcangle_it	2.043
r_angle_refined_deg	1.886
r_mcbond_it	1.278
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.263
r_symmetry_hbond_refined	0.257
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.145
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8820
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	189

Software

Software
Software Name	Purpose
DNA	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.