Experiment: 2NTV

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	12% MPD, 4% DMSO, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.232	α = 90
b = 100.019	β = 90
c = 186.622	γ = 90

Symmetry
Space Group	I 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	121	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97	APS	23-ID-B

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	50	99.5	0.068	10	7		49856

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	2.1	2.18	95.6		0.569	0.88	2	4.9	4735

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 (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 1ZID	2.1	19.89	49775	2527	99.37	0.22	0.219	0.22	0.244	0.24	RANDOM	40.098

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]
0.02					-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.943
r_dihedral_angle_4_deg	22.179
r_dihedral_angle_3_deg	20.485
r_dihedral_angle_1_deg	7.345
r_scangle_it	3.092
r_angle_refined_deg	2.146
r_scbond_it	1.948
r_mcangle_it	1.224
r_mcbond_it	0.648
r_chiral_restr	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.943
r_dihedral_angle_4_deg	22.179
r_dihedral_angle_3_deg	20.485
r_dihedral_angle_1_deg	7.345
r_scangle_it	3.092
r_angle_refined_deg	2.146
r_scbond_it	1.948
r_mcangle_it	1.224
r_mcbond_it	0.648
r_chiral_restr	0.319
r_nbtor_refined	0.313
r_nbd_refined	0.258
r_symmetry_vdw_refined	0.219
r_xyhbond_nbd_refined	0.208
r_symmetry_hbond_refined	0.15
r_bond_refined_d	0.017
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4016
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	110

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
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.