3JRD | pdb_00003jrd

Crystal structure of Fis bound to 27 bp DNA F25 containing T2A3 sequence at center

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IV5

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, 38% PEG 400, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4	69.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.296	α = 90
b = 93.076	β = 90
c = 155.097	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	3.1	90	91	0.186	7.4	3.9		10882

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	3.1	3.21	93.8		0.666		4	1068

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	3IV5	3.1	79.81	10795	512	90.03	0.245	0.242	0.24	0.291	0.29	RANDOM	82.247

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	45.751
r_dihedral_angle_4_deg	27.378
r_dihedral_angle_3_deg	17.914
r_dihedral_angle_1_deg	5.825
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	4.395
MAIN-CHAIN BOND REFINED ATOMS (A''2)	3.462
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	3.263
SIDE-CHAIN BOND REFINED ATOMS (A''2)	2.21
r_angle_refined_deg	2.094
r_angle_other_deg	1.136
MAIN-CHAIN BOND OTHER ATOMS (A''2)	0.59
r_symmetry_hbond_refined	0.289
r_nbtor_refined	0.217
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.213
r_nbd_other	0.206
r_symmetry_vdw_other	0.187
r_xyhbond_nbd_refined	0.152
r_nbtor_other	0.095
CHIRAL-CENTER RESTRAINTS (A''3)	0.082
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
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