7AIA

Complex of human GDAP1 with hexadecanedioic acid

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Lithium sulfate, 0.1 M bis-Tris pH 5.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.74	67.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.045	α = 90
b = 114.914	β = 90
c = 116.866	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		2019-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9795	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.2	45.63	99.7	0.998	12.72	6.6		50525

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.279			0.657

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	GDAP1	2.2	45.629	50524	2011	99.735	0.203	0.2022	0.2299	70.524

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]
-2.705			4.656		-1.952

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.468
r_dihedral_angle_4_deg	19.949
r_dihedral_angle_3_deg	16.677
r_lrange_it	11.846
r_lrange_other	11.846
r_scangle_it	6.935
r_scangle_other	6.877
r_dihedral_angle_1_deg	6.538
r_mcangle_other	5.202
r_mcangle_it	5.2
r_scbond_it	4.678
r_scbond_other	4.568
r_mcbond_it	3.406
r_mcbond_other	3.4
r_angle_refined_deg	1.79
r_angle_other_deg	1.471
r_ext_dist_refined_d	0.354
r_symmetry_nbd_refined	0.273
r_nbd_other	0.251
r_nbd_refined	0.231
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_refined	0.161
r_ncsr_local_group_1	0.117
r_symmetry_xyhbond_nbd_other	0.094
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4162
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	74

Software

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