Experiment: 1Y98

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T15	pdb entry 1T15

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	AMMONIUM SULPHATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.118	α = 90
b = 113.118	β = 90
c = 121.876	γ = 120

Symmetry
Space Group	P 61 2 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	ADSC QUANTUM 4		2004-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	1.0000	NSLS	X12B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	20	99.1	0.133	17.53	11		16294			47.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	99.4		0.372	2.68	6.4	1593

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1T15	2.5	19.59	16399	15278	1008	99.31	0.2337	0.236	0.2337	0.23	0.2696	0.27	RANDOM	53.275

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]
-0.34	-0.17		-0.34		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.937
r_dihedral_angle_3_deg	19.001
r_dihedral_angle_4_deg	17.557
r_dihedral_angle_1_deg	7.927
r_scangle_it	3.17
r_scbond_it	1.894
r_angle_refined_deg	1.781
r_mcangle_it	1.679
r_mcbond_it	0.947
r_symmetry_vdw_refined	0.435

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.937
r_dihedral_angle_3_deg	19.001
r_dihedral_angle_4_deg	17.557
r_dihedral_angle_1_deg	7.927
r_scangle_it	3.17
r_scbond_it	1.894
r_angle_refined_deg	1.781
r_mcangle_it	1.679
r_mcbond_it	0.947
r_symmetry_vdw_refined	0.435
r_nbtor_refined	0.329
r_nbd_refined	0.264
r_xyhbond_nbd_refined	0.188
r_chiral_restr	0.117
r_symmetry_hbond_refined	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1786
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	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.