Experiment: 2ZYT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZPT	PDB ENTRY 2ZPT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	16% PEG 10000, 10mM dithiothreitol, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.156	α = 90
b = 65.154	β = 104.2
c = 46.824	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU JUPITER 210	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	1.55	50	81.4	0.093	0.093	14.2	3.2	55335	55335

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	1.55	1.61	42.8		0.527	0.527	1.2	2.5	2890

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZPT	1.55	34.67	52526	2782	81.29	0.19193	0.19097	0.21	RANDOM	22.943

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.094
r_dihedral_angle_4_deg	19.716
r_dihedral_angle_3_deg	12.737
r_dihedral_angle_1_deg	5.117
r_scangle_it	2.275
r_scbond_it	1.463
r_angle_refined_deg	1.2
r_mcangle_it	0.946
r_mcbond_it	0.593
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.094
r_dihedral_angle_4_deg	19.716
r_dihedral_angle_3_deg	12.737
r_dihedral_angle_1_deg	5.117
r_scangle_it	2.275
r_scbond_it	1.463
r_angle_refined_deg	1.2
r_mcangle_it	0.946
r_mcbond_it	0.593
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.192
r_symmetry_hbond_refined	0.115
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2440
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
BBS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.