4KQD | pdb_00004kqd

The crystal Structure of the N-terminal PAS domain of the F plasmid TraJ

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277.15	2M Ammonium sulphate, 0.1 M sodium citrate, 5% glycerol, 5 mM DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.228	α = 90
b = 95.228	β = 90
c = 102.041	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315r			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.11584, 0.979566, 0.953697, 0.979685	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.55	82.47	99.8	0.058	0.051		10.5	75906	75754	243.5	8.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	97.2		0.708	0.609	2.3	6.1

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	MAD	THROUGHOUT	1.55	47.66	71829	3797	99.71	0.16116	0.16027	0.17	0.17799	0.18	RANDOM	27.162

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]
0.14	0.14		0.14		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.907
r_sphericity_free	27.46
r_dihedral_angle_4_deg	15.427
r_dihedral_angle_3_deg	14.368
r_sphericity_bonded	6.919
r_dihedral_angle_1_deg	6.411
r_rigid_bond_restr	2.357
r_mcangle_it	1.822
r_scbond_it	1.821
r_mcbond_it	1.447
r_mcbond_other	1.447
r_angle_refined_deg	1.269
r_angle_other_deg	0.757
r_chiral_restr	0.085
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3810
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	30

Software

Software
Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling