8TTR | pdb_00008ttr

CA9 mimic bound to SH7

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VKG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	CA9 mimic crystals were obtained in sitting drop plates with seeding. The protein concentration was about 5.5 mg/mL, 150 nL was added to 120 nL of reservoir and 30 nL of seeds. The reservoir consisted of 2.6 to 2.8 M ammonium sulfate with 100 mM tris buffer at pH 8.0 to 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.16	α = 90
b = 41.514	β = 104.131
c = 72.065	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2020-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953724	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.45	41.5	100	0.166	0.049	0.999	13.4	12.5		43133

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47			2.175	0.63	0.556	1.7

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	FREE R-VALUE	1.45	40.917	43114	2169	99.965	0.164	0.1629	0.1636	0.1866	0.188	14.321

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]
-0.088		-0.408	0.261		0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.994
r_dihedral_angle_3_deg	13.488
r_dihedral_angle_2_deg	8.78
r_dihedral_angle_1_deg	6.679
r_lrange_it	5.275
r_lrange_other	5.186
r_scangle_it	4.151
r_scangle_other	4.151
r_scbond_it	2.705
r_scbond_other	2.697
r_mcangle_other	2.474
r_mcangle_it	2.472
r_angle_refined_deg	1.835
r_mcbond_it	1.607
r_mcbond_other	1.606
r_angle_other_deg	0.776
r_symmetry_xyhbond_nbd_other	0.325
r_nbd_other	0.258
r_symmetry_nbd_refined	0.24
r_xyhbond_nbd_refined	0.209
r_nbd_refined	0.201
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.166
r_metal_ion_refined	0.121
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2061
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	51

Software

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