3JRE | pdb_00003jre

Crystal structure of Fis bound to 27 bp DNA F26 containing A-tract at center

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.2 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 36% PEG 400, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.638	α = 90
b = 94.215	β = 90
c = 155.272	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	100	CCD	ADSC QUANTUM 315		2008-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.000	APS	24-ID-C

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	3.15	90	83.9	0.196	5.7	5.6		9497

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	3.15	3.26	86.1		0.717		5.7	950

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3IV5	THROUGHOUT	3.17	80.58	9418	440	82	0.21	0.209	0.21	0.232	0.23	RANDOM	69.334

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.8
r_dihedral_angle_4_deg	19.309
r_dihedral_angle_3_deg	18.497
r_dihedral_angle_1_deg	5.966
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	4.167
MAIN-CHAIN BOND REFINED ATOMS (A''2)	3.327
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	3.076
r_angle_refined_deg	2.061
SIDE-CHAIN BOND REFINED ATOMS (A''2)	1.982
r_angle_other_deg	1.114
MAIN-CHAIN BOND OTHER ATOMS (A''2)	0.507
r_symmetry_hbond_refined	0.257
r_nbtor_refined	0.21
r_nbd_other	0.203
r_nbd_refined	0.198
r_symmetry_vdw_other	0.165
r_xyhbond_nbd_refined	0.128
r_symmetry_vdw_refined	0.121
r_nbtor_other	0.096
CHIRAL-CENTER RESTRAINTS (A''3)	0.077
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	1505
Nucleic Acid Atoms	1101
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing