2GAJ

Structure of Full Length Topoisomerase I from Thermotoga maritima in monoclinic crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GAI	PDB ENTRY 2GAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	34 % Jeffamine M-600, 100 mM MES/NaOH, 64 mM Sodium Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.049	α = 90
b = 142.714	β = 90.84
c = 127.638	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 4	mirrors	2004-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.2815	ESRF	ID29

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	1.95	45	99.6	0.12	8.2		116615	116615

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	1.95	2.05	99.1		0.44	2.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2GAI	1.95	15	116577	110740	5837	99.6	0.197	0.197	0.195	0.246	RANDOM	9.845

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]
0.74		-0.47	0.22		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.217
r_dihedral_angle_4_deg	19.901
r_dihedral_angle_3_deg	15.918
r_dihedral_angle_1_deg	6
r_scangle_it	4.282
r_scbond_it	2.919
r_angle_refined_deg	1.999
r_mcangle_it	1.569
r_mcbond_it	1.435
r_angle_other_deg	1.082
r_mcbond_other	0.265
r_symmetry_hbond_refined	0.245
r_symmetry_vdw_other	0.216
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.2
r_nbd_other	0.179
r_nbtor_refined	0.179
r_symmetry_vdw_refined	0.133
r_chiral_restr	0.117
r_nbtor_other	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9428
Nucleic Acid Atoms
Solvent Atoms	877
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing