8UFW | pdb_00008ufw

CA9 mimic with SLC compound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MU3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	The protein was set up in MRC2 plates in 100 nL plus 100 nL drops with the protein at 5 mg/mL with reservoir solutions being 2.6 to 2.9 M ammonium sulfate and 100 mM Tris buffer at pH 8.3 to 8.9

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.985	α = 90
b = 41.414	β = 103.968
c = 72.309	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		2021-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953659	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	1.21	41.4	97.5	0.072	0.03	0.999	12.4	6.7		70793

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	1.21	1.24	83.5		0.779	0.326	0.736	2.3	6.3

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	1.215	39.664	70773	3563	97.169	0.114	0.1129	0.1121	0.143	0.1425	15.42

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]
-0.368		0.476	0.72		-0.524

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.553
r_lrange_it	13.814
r_dihedral_angle_3_deg	13.063
r_lrange_other	12.916
r_scangle_it	10.794
r_scangle_other	10.567
r_mcangle_other	7.927
r_mcangle_it	7.905
r_scbond_it	7.397
r_scbond_other	7.224
r_dihedral_angle_1_deg	6.43
r_mcbond_it	6.272
r_dihedral_angle_2_deg	5.82
r_mcbond_other	4.989
r_rigid_bond_restr	4.848
r_angle_refined_deg	1.763
r_symmetry_xyhbond_nbd_other	0.589
r_angle_other_deg	0.584
r_symmetry_nbd_refined	0.339
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.228
r_symmetry_nbd_other	0.206
r_nbd_other	0.199
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.156
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.087
r_metal_ion_refined	0.056
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2066
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	40

Software

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