2G7O | pdb_00002g7o

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	297	30% PEG 400, 0.1M MES pH 6.5, 2mM DTT, 0.5M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.733	α = 90
b = 51.733	β = 90
c = 49.585	γ = 90

Symmetry
Space Group	I 4

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		2005-06-14	M	SINGLE WAVELENGTH
2	1	x-ray	105	CCD	ADSC QUANTUM 210		2005-07-20	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11697	ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.979617, 1.019440	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	1.4	36.58	99.1	0.039	27.6	3.6	12828	12828

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)
1,2	1.4	1.42	86.6	86.6	0.371	3.12	2.8	548

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.4	36.58	12827	12827	626	99.43	0.195	0.195	0.193	0.23	0.224	0.26	RANDOM	17.335

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.961
r_dihedral_angle_4_deg	28.655
r_dihedral_angle_3_deg	10.366
r_dihedral_angle_1_deg	3.684
r_scangle_it	3.528
r_scbond_it	2.233
r_mcangle_it	1.243
r_angle_refined_deg	1.233
r_mcbond_it	0.744
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.961
r_dihedral_angle_4_deg	28.655
r_dihedral_angle_3_deg	10.366
r_dihedral_angle_1_deg	3.684
r_scangle_it	3.528
r_scbond_it	2.233
r_mcangle_it	1.243
r_angle_refined_deg	1.233
r_mcbond_it	0.744
r_nbtor_refined	0.307
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.123
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	544
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.