Experiment: 3INY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V41

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Hanging drops were prepared mixing 1 microL of protein solution and 1 microL of reservoir solution containing 19% ammonium sulfate and 0.5 M sodium citrate pH 5.6. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.59	73.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.748	α = 90
b = 138.748	β = 90
c = 159.366	γ = 120

Symmetry
Space Group	H 3 2

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	MAR CCD 165 mm		2008-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.4310	LNLS	D03B-MX1

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	2.75	47.95	99.1	0.081	0.081	11	3.9	14793		2	2	65

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)
	2.75		99.1		0.081	0.081	3.91	3.9	15340

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1V41	2.75	43.69	2	2	14566	765	98.66	0.2123	0.2123	0.20933	0.21	0.2693	0.26	RANDOM	43.404

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]
0.01	0.01		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.43
r_dihedral_angle_4_deg	26.683
r_dihedral_angle_3_deg	25.884
r_dihedral_angle_1_deg	12.423
r_scangle_it	5.604
r_scbond_it	3.767
r_angle_refined_deg	3.57
r_mcangle_it	2.837
r_mcbond_it	1.751
r_nbtor_refined	0.368

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.43
r_dihedral_angle_4_deg	26.683
r_dihedral_angle_3_deg	25.884
r_dihedral_angle_1_deg	12.423
r_scangle_it	5.604
r_scbond_it	3.767
r_angle_refined_deg	3.57
r_mcangle_it	2.837
r_mcbond_it	1.751
r_nbtor_refined	0.368
r_nbd_refined	0.322
r_symmetry_vdw_refined	0.262
r_chiral_restr	0.226
r_xyhbond_nbd_refined	0.226
r_symmetry_hbond_refined	0.21
r_bond_refined_d	0.04
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2251
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	26

Software

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