Experiment: 2DY2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	Tris, MgCl2, PEG 1500, pH 6.0, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.996	α = 90
b = 74.996	β = 90
c = 153.611	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH		2005-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.115	MAX II	I911-3

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	2.26	31.77	99.8	0.065	0.065	7.9	5.6		15045

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)
1	2.26	2.38	100		0.294	0.294	2.6	5.6	2174

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZV2	2.26	31.77	15043	760	99.73	0.194	0.192	0.241	RANDOM	42.279

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]
-2.07	-1.04		-2.07		3.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.623
r_dihedral_angle_4_deg	19.614
r_dihedral_angle_3_deg	17.038
r_dihedral_angle_1_deg	7.483
r_scangle_it	2.664
r_scbond_it	1.775
r_angle_refined_deg	1.583
r_mcangle_it	1.279
r_mcbond_it	0.748
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.623
r_dihedral_angle_4_deg	19.614
r_dihedral_angle_3_deg	17.038
r_dihedral_angle_1_deg	7.483
r_scangle_it	2.664
r_scbond_it	1.775
r_angle_refined_deg	1.583
r_mcangle_it	1.279
r_mcbond_it	0.748
r_nbtor_refined	0.309
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.182
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_metal_ion_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2530
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	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.