3M8K | pdb_00003m8k

Protein structure of type III plasmid segregation TubZ

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	4 M NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.601	α = 90
b = 131.601	β = 90
c = 76.116	γ = 120

Symmetry
Space Group	H 3

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 315r	KOHZU: Double Crystal Si(111)	2009-01-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.97963,1.01995,0.97974	ALS	8.3.1

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	2.3	65.79	99.7	0.062	19.4	6.1	21805	21740		3

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)
	2.3	2.42	100		0.271	4.6	6.2

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	2.3	65.79	20625	1111	99.66	0.21542	0.21363	0.229	0.25077	0.2698	RANDOM	53.279

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]
-2.51	-1.25		-2.51		3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.249
r_dihedral_angle_3_deg	18.455
r_dihedral_angle_4_deg	17.268
r_dihedral_angle_1_deg	5.956
r_scangle_it	1.825
r_angle_refined_deg	1.264
r_scbond_it	1.176
r_mcangle_it	0.946
r_mcbond_it	0.568
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.225
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.096
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3116
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling