3JRI | pdb_00003jri

Crystal structure of Fis bound to 27 bp non consensus sequence DNA F23

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	0.3 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
3.97	68.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.222	α = 90
b = 92.635	β = 90
c = 154.863	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		2007-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.000	ALS	8.2.2

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	99.7	0.144	8.2	6.4		11811

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	97.6		0.605		5.1	1108

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	3.11	79.56	11756	559	99.57	0.232	0.23	0.23	0.271	0.27	RANDOM	85.056

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	42.141
r_dihedral_angle_3_deg	19.085
r_dihedral_angle_4_deg	15.777
r_dihedral_angle_1_deg	5.901
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	1.918
r_angle_refined_deg	1.842
SIDE-CHAIN BOND REFINED ATOMS (A''2)	1.271
r_angle_other_deg	1.096
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	0.871
MAIN-CHAIN BOND REFINED ATOMS (A''2)	0.732
r_nbd_refined	0.227
r_nbtor_refined	0.217
r_nbd_other	0.206
r_symmetry_vdw_other	0.201
r_symmetry_hbond_refined	0.184
r_symmetry_vdw_refined	0.116
r_xyhbond_nbd_refined	0.113
MAIN-CHAIN BOND OTHER ATOMS (A''2)	0.109
r_nbtor_other	0.093
CHIRAL-CENTER RESTRAINTS (A''3)	0.072
r_bond_refined_d	0.015
r_bond_other_d	0.005
r_gen_planes_refined	0.005
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