2HRI | pdb_00002hri

A parallel stranded human telomeric quadruplex in complex with the porphyrin TMPyP4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A5R	PDB ENTRY 2A5R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	285	500 mM ammonium sulphate, 80 mM lithium sulphate, 80 mM sodium chloride, 80 mM potassium chloride, 20mM potassium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.29	α = 90
b = 61.99	β = 90
c = 61.4	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	IMAGE PLATE	RIGAKU RAXIS IV	osmic mirrors	2006-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	2.09	28.35	99.9	0.043	18.2	5.07	4443	4443			45

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	2.09	2.16	99.5		0.201	6.5	4.9	433

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 (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 2A5R	2.09	28.35	4239	4239	204	99.82	0.20062	0.20062	0.19829	0.19	0.24833	0.22	RANDOM	24.671

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]
-2.19			2.06		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.577
r_angle_refined_deg	2.16
r_scbond_it	1.874
r_nbd_refined	0.322
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.262
r_symmetry_vdw_refined	0.249
r_xyhbond_nbd_refined	0.173
r_metal_ion_refined	0.107
r_chiral_restr	0.092
r_gen_planes_refined	0.017
r_bond_refined_d	0.013
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	462
Solvent Atoms	46
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing