3CDM | pdb_00003cdm

Structural adaptation and conservation in quadruplex-drug recognition

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KF1	PDB ENTRY 1KF1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	283	333mM ammonium sulfate, 10mM magnesium chloride, 50mM sodium chloride, 50mM potassium chloride, 50mM potassium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.575	α = 90
b = 43.084	β = 103.58
c = 56.937	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210	Monochromator	2007-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9785	ESRF	ID14-1

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	28.69	91	0.036	17.9	2.86	10055	10055			46

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)
	2.1	2.18	95.9		0.116	6.4	2.94	1041

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 (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 1KF1	2.1	10	9497	9497	478	91.26	0.23409	0.23409	0.2224	0.29491	0.2833	RANDOM	26.776

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]
0.51		0.53	-1.42		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.226
r_angle_refined_deg	2.804
r_scbond_it	2.779
r_nbd_refined	0.342
r_nbtor_refined	0.331
r_xyhbond_nbd_refined	0.219
r_symmetry_vdw_refined	0.17
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.125
r_metal_ion_refined	0.107
r_bond_refined_d	0.019
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	950
Solvent Atoms	158
Heterogen Atoms	256

Software

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