3JRC | pdb_00003jrc

Crystal structure of Fis bound to 27 bp DNA F29 containing 5 G/Cs 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	0.25 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 40% PEG 400, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.48	α = 90
b = 93.64	β = 90
c = 155.63	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		2007-01-01	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	93.1	0.144	8.4	8		11654

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	61.2		0.626		4.5	735

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	3.08	80.32	10306	488	83.29	0.232	0.23	0.23	0.27	0.28	RANDOM	63.353

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	39.028
r_dihedral_angle_4_deg	19.213
r_dihedral_angle_3_deg	18.037
r_dihedral_angle_1_deg	5.252
r_angle_refined_deg	1.215
r_angle_other_deg	0.971
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	0.627
SIDE-CHAIN BOND REFINED ATOMS (A''2)	0.514
MAIN-CHAIN BOND REFINED ATOMS (A''2)	0.355
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	0.249
r_nbtor_refined	0.2
r_nbd_other	0.199
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.152
r_symmetry_vdw_other	0.137
r_xyhbond_nbd_refined	0.122
r_symmetry_vdw_refined	0.099
r_nbtor_other	0.081
CHIRAL-CENTER RESTRAINTS (A''3)	0.052
MAIN-CHAIN BOND OTHER ATOMS (A''2)	0.024
r_bond_other_d	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1501
Nucleic Acid Atoms	1101
Solvent Atoms	2
Heterogen Atoms

Software

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