8RPD | pdb_00008rpd

Crystal structure of the SMA homodimer

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1M HEPES buffer pH 7.0, 1M Succinic acid and 1% w/v PEG2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.816	α = 90
b = 56.816	β = 90
c = 59.78	γ = 120

Symmetry
Space Group	P 31 1 2

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 EIGER2 XE 16M		2022-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

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	2.13	49.2	98.5	0.107	0.094	0.994	5	3.4		6216			33.24

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	2.13	2.19	82.1		0.835	0.768	0.6	1	3.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.15	28.424	6154	311	99.805	0.194	0.1903	0.1928	0.2538	0.2563	RANDOM	37.882

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]
-1.139	-0.57		-1.139		3.695

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.739
r_dihedral_angle_6_deg	13.079
r_lrange_it	7.412
r_lrange_other	7.368
r_dihedral_angle_1_deg	7.334
r_scangle_it	6.121
r_scangle_other	6.116
r_mcangle_it	4.622
r_mcangle_other	4.619
r_dihedral_angle_2_deg	4.533
r_scbond_it	4.045
r_scbond_other	4.041
r_mcbond_it	3.402
r_mcbond_other	3.368
r_angle_refined_deg	1.725
r_angle_other_deg	0.576
r_symmetry_xyhbond_nbd_refined	0.239
r_symmetry_nbd_other	0.207
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.16
r_nbd_other	0.141
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.08
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	898
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing