4XTJ | pdb_00004xtj

N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM KCl plus 100 mM NaCl condition

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EI1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	15-25% (v/v) PEG 3350, 2 mM MgCl2, 100 mM KCl, 100 mM NaCl, 100 mM Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.52	α = 90
b = 140.91	β = 90
c = 79.84	γ = 90

Symmetry
Space Group	C 2 2 21

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 315r		2012-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.92	35.23	99.6	0.061	0.029	0.999	18.5	5.3		37803			27.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.97	96.2		0.915	0.434	0.699	1.9	5.3	2668

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1EI1	1.92	35.23	35855	1947	99.51	0.1854	0.1837	0.2181	0.2034	RANDOM	36.3

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]
0.61			1.51		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.542
r_dihedral_angle_4_deg	17.179
r_dihedral_angle_3_deg	12.522
r_dihedral_angle_1_deg	5.236
r_mcangle_it	1.614
r_angle_refined_deg	1.271
r_mcbond_other	1.083
r_mcbond_it	1.082
r_angle_other_deg	0.774
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2919
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	35

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing