Experiment: 4HT2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JD0	PDB ENTRY 1JD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	0.1M ammonium citrate with pH 5.0 and 16% of PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.709	α = 81.78
b = 67.261	β = 84.01
c = 80.689	γ = 86.48

Symmetry
Space Group	P 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	MAR CCD 165 mm	Mirror Bent, vertically focussing	2011-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8123	EMBL/DESY, HAMBURG	X13

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	1.45	27.164	97.1	0.039	0.039	14.1	4		166179			11.3

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	1.45	1.53	95.6		0.219	0.219	3.4	4	23905

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JD0	1.45	26.5	166179	166177	16455	97.08	0.154	0.154	0.15	0.188	RANDOM	12.981

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]
-0.33	0.05	0.02	-0.1	0.49	0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.671
r_dihedral_angle_4_deg	18.181
r_dihedral_angle_3_deg	13.132
r_dihedral_angle_1_deg	7.373
r_scangle_it	4.448
r_scbond_it	3.129
r_angle_refined_deg	2.462
r_mcangle_it	2.214
r_mcbond_it	1.432
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.671
r_dihedral_angle_4_deg	18.181
r_dihedral_angle_3_deg	13.132
r_dihedral_angle_1_deg	7.373
r_scangle_it	4.448
r_scbond_it	3.129
r_angle_refined_deg	2.462
r_mcangle_it	2.214
r_mcbond_it	1.432
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.228
r_chiral_restr	0.2
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.167
r_metal_ion_refined	0.037
r_bond_refined_d	0.031
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8392
Nucleic Acid Atoms
Solvent Atoms	1504
Heterogen Atoms	165

Software

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