3LPV | pdb_00003lpv

X-ray crystal structure of duplex DNA containing a cisplatin 1,2-d(GpG) intrastrand cross-link

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	120 mM Magnesium Acetate, 50 mM Sodium Cacodylate pH 6.5, 28% w/v PEG-4000, 1 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.303	α = 80.06
b = 35.425	β = 84.09
c = 45.128	γ = 81.77

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	CCD	MARMOSAIC 325 mm CCD	Rh coated flat mirror, toroidal focusing mirror	2009-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

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	1.77	50	96	0.092	15.6	2.9	17639	17639

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)
	1.77	1.83	85.2		0.389		2.5

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	1AIO	1.77	44.31	17624	16745	891	96.25	0.17342	0.17212	0.17	0.19788	0.2	RANDOM	39.042

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]
-0.53	0.09	1.75	-0.34	1.31	0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.84
r_scbond_it	1.895
r_angle_refined_deg	1.883
r_mcbond_it	0.315
r_nbd_other	0.265
r_nbtor_refined	0.263
r_symmetry_hbond_refined	0.216
r_symmetry_vdw_other	0.166
r_xyhbond_nbd_refined	0.161
r_symmetry_vdw_refined	0.146
r_nbd_refined	0.105
r_chiral_restr	0.08
r_nbtor_other	0.074
r_metal_ion_refined	0.041
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.001
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_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
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	972
Solvent Atoms	148
Heterogen Atoms	10

Software

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