8RPE | pdb_00008rpe

Crystal structure of the SMA:VH1 Complex at 1.2 A resolution

X-RAY DIFFRACTION

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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, HANGING DROP	5.5	293	Bis-Tris buffer at pH 5.5 and 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.813	α = 90
b = 53.544	β = 90
c = 99.07	γ = 90

Symmetry
Space Group	P 21 21 21

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		2023-07-29	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	1.2	49.54	97.8	0.036	0.022	0.999	22.1	6.2		63942			9.04

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	79.7		0.167	0.127	4.8

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	1.2	47.149	63861	3214	97.638	0.113	0.1118	0.1112	0.1437	0.1436	RANDOM	11.043

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]
0.291			0.041		-0.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.899
r_lrange_it	12.546
r_lrange_other	10.803
r_dihedral_angle_3_deg	10.397
r_dihedral_angle_2_deg	9.307
r_dihedral_angle_1_deg	7.109
r_scangle_it	6.937
r_scangle_other	6.934
r_mcangle_other	5.068
r_mcangle_it	5.067
r_scbond_it	5.012
r_scbond_other	5.01
r_rigid_bond_restr	4.221
r_mcbond_it	3.519
r_mcbond_other	3.514
r_angle_refined_deg	1.976
r_angle_other_deg	0.725
r_xyhbond_nbd_other	0.321
r_symmetry_xyhbond_nbd_refined	0.317
r_symmetry_nbd_refined	0.29
r_nbd_refined	0.254
r_xyhbond_nbd_refined	0.25
r_symmetry_nbd_other	0.206
r_nbd_other	0.203
r_nbtor_refined	0.179
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1779
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	28

Software

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