1G3X | pdb_00001g3x

INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.5 mM duplex, 1mM drug-peptide adduct, 20 mM NaCacodylate, 100 mM MgCl2, 45% MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.471	α = 90
b = 68.365	β = 90
c = 77.362	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	110	IMAGE PLATE	MARRESEARCH		1998-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	2.7	30	91.2	0.054	13.3	8.8		12155

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)
	2.7	3.2	90.3		0.223		1.64

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	20	8086	921	89.05	0.22476	0.22005	0.26607	RANDOM	37.54

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]
-4.66			-1.21		5.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	31.341
r_dihedral_angle_1_deg	3.978
r_angle_refined_deg	2.409
r_scangle_it	1.875
r_scbond_it	1.37
r_mcangle_it	1.136
r_mcbond_it	0.457
r_symmetry_hbond_refined	0.152
r_nbd_refined	0.129
r_xyhbond_nbd_refined	0.128
r_symmetry_vdw_refined	0.119
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	48
Nucleic Acid Atoms	2897
Solvent Atoms	61
Heterogen Atoms	49

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling