8Q1W | pdb_00008q1w

TtX183B - A c-type cytochrome domain from the Teredinibacter turnerae protein TERTU_2913

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		TtX183A model, PDB code not yet avilable

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	15-25% (w/v) PEG 6000, 200 mM sodium acetate pH 5.0 and 200 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.548	α = 90.48
b = 38.659	β = 90.591
c = 44.049	γ = 94.481

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2019-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96884	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.8	38.54	96.8	0.202	0.286	0.202	0.816	3.4	2.3		22802

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84			0.765	1.082	0.765	0.562		2.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	38.457	22802	1135	96.844	0.197	0.195	0.1993	0.2404	0.2446	12.22

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]
0.158	-0.284	-0.748	0.033	-0.832	-0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.376
r_dihedral_angle_6_deg	14.173
r_dihedral_angle_1_deg	5.984
r_lrange_it	3.621
r_lrange_other	3.606
r_angle_refined_deg	2.4
r_scangle_other	2.341
r_scangle_it	2.34
r_dihedral_angle_2_deg	2.216
r_mcangle_it	1.52
r_mcangle_other	1.52
r_scbond_it	1.425
r_scbond_other	1.409
r_mcbond_it	0.902
r_mcbond_other	0.894
r_angle_other_deg	0.54
r_nbd_refined	0.332
r_symmetry_nbd_other	0.203
r_nbd_other	0.176
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.074
r_symmetry_nbd_refined	0.072
r_chiral_restr	0.062
r_gen_planes_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1745
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	134

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction