Experiment: 4R45

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	285	1 mM DNA, 50 mM potassium cacodylate, 40 mM potassium chloride, 50 mM magnesium chloride hexahydrate, 2.5 mM spermine, 5% v/v MPD, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.646	α = 104.5
b = 28.3	β = 94.19
c = 45.719	γ = 113.42

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	PIXEL	DECTRIS PILATUS 200K		2013-12-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.9	25.02	94.89	0.0628	7.81	1.7	9497	9011	2	2	49.29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	95.66		0.1227	2.66	1.5	909

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2HBN	1.9	25.02	9075	8599	412	94.75	0.28797	0.28562	0.34003	RANDOM	14.068

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]
-0.06	-0.02	0.06		0.03	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	4.991
r_long_range_B_other	4.348
r_angle_other_deg	1.652
r_angle_refined_deg	1.049
r_scangle_other	1.02
r_scbond_it	0.619
r_scbond_other	0.619
r_chiral_restr	0.075
r_gen_planes_refined	0.014
r_bond_refined_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	4.991
r_long_range_B_other	4.348
r_angle_other_deg	1.652
r_angle_refined_deg	1.049
r_scangle_other	1.02
r_scbond_it	0.619
r_scbond_other	0.619
r_chiral_restr	0.075
r_gen_planes_refined	0.014
r_bond_refined_d	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	506
Solvent Atoms	143
Heterogen Atoms	5

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

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.