1MW8 | pdb_00001mw8

Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3'

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ECL	H365R mutant, apo form

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	287	ammonium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.392	α = 90
b = 79.148	β = 90
c = 141.798	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	103	CCD	MARRESEARCH		2001-12-07	M	SINGLE WAVELENGTH
2	1	103	CCD	MARRESEARCH		2002-02-16

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.95	APS	5ID-B
2	SYNCHROTRON	APS BEAMLINE 5ID-B	0.95	APS	5ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	35	95.5	0.069	0.061	7.7	3.9		53723

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	H365R mutant, apo form	1.9	70.71	52986	2846	97.89	0.22595	0.22346	0.23	0.27257	0.28	RANDOM	31.266

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			1.16		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.637
r_dihedral_angle_1_deg	3.751
r_scangle_it	3.329
r_scbond_it	1.956
r_mcangle_it	1.411
r_angle_refined_deg	1.321
r_mcbond_it	0.751
r_angle_other_deg	0.726
r_xyhbond_nbd_other	0.305
r_nbd_refined	0.279
r_symmetry_vdw_refined	0.275
r_symmetry_hbond_refined	0.275
r_xyhbond_nbd_refined	0.242
r_nbd_other	0.24
r_symmetry_vdw_other	0.235
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_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	4621
Nucleic Acid Atoms	126
Solvent Atoms	553
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MAR345	data collection
CCP4	data scaling
CNS	phasing