1ZRF | pdb_00001zrf

4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6C;17G]ICAP38 DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZRC	PDB entry 1ZRC, with only central 20 bps

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	295	2mM cAMP, 0.1M MES, 0.2M NaCl, 0.05M MgCl2, 5% PEG 8000, 15% Dioxane, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.778	α = 90
b = 77.745	β = 90
c = 154.813	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	108	CCD	ADSC QUANTUM 315		2005-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.100	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	2.1	32.9	97.3	0.109		6.3	44370	42032			22.3

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		99.1	0.886		5.5

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 (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 1ZRC, with only central 20 bps	2.1	32.9	44200	42032	4239	95.1	0.242	0.242	0.225	0.2433	0.266	0.2828	RANDOM	45.93

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]
-4.14			-3.3		7.45

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.5
c_angle_deg	1.1
c_improper_angle_d	0.89
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3186
Nucleic Acid Atoms	1484
Solvent Atoms	266
Heterogen Atoms	118

Software

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