2HBN | pdb_00002hbn

Crystallization of the Tl+-form of the Oxytricha nova G-quadruplex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	1.5 mM DNA, 50 mM Potassium cacodylate, 10 mM Magnesium acetate, 40 mM Potassium acetate, 5% (v/v) MPD mixed with equal amount of 35% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.375	α = 90
b = 48.21	β = 90
c = 96.198	γ = 90

Symmetry
Space Group	P 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	100	CCD	ADSC QUANTUM 315		2005-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.979	NSLS	X25

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	1.55	43.11	95	0.187	4.4	3.6	19237	18241	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.55	1.61	98.1		1	3.7	3522

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-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 1JRN	1.55	43.11	18241	18241	930	94.82	0.228	0.226	0.2298	0.248	0.2493	RANDOM	29.02

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]
-0.04			0.29		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	9.487
r_sphericity_bonded	3.081
r_scangle_it	2.745
r_scbond_it	2.166
r_angle_refined_deg	1.903
r_rigid_bond_restr	1.86
r_nbtor_refined	0.283
r_symmetry_hbond_refined	0.23
r_nbd_refined	0.18
r_xyhbond_nbd_refined	0.117
r_symmetry_vdw_refined	0.112
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1012
Solvent Atoms	44
Heterogen Atoms	10

Software

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