3D8A | pdb_00003d8a

Co-crystal structure of TraM-TraD complex.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	30% PEG 2000, 100 mM tris HCl pH 8.5, 200 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.246	α = 90
b = 142.246	β = 90
c = 70.95	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	105	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11588	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.55	71.07	100			17494	17494

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.56	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2G07	2.55		17453	16609	884	99.95	0.21973	0.21973	0.21767	0.21	0.25746	RANDOM	41.975

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]
0.13	0.06		0.13		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.775
r_dihedral_angle_4_deg	18.979
r_dihedral_angle_3_deg	16.934
r_dihedral_angle_1_deg	4.401
r_scangle_it	1.575
r_angle_refined_deg	1.058
r_scbond_it	0.997
r_mcangle_it	0.682
r_mcbond_it	0.392
r_nbtor_refined	0.299
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.203
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.083
r_bond_refined_d	0.011
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	4456
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing