7ZKW

Crystal structure of cystinosin from Arabidopsis thaliana in complex with Cystine and sybody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZK1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.5	293	28% PEG 500DME, 100 mM MES-NaOH, pH 5.50, 150 mM K-formate

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 283.372	α = 90
b = 64.065	β = 99.946
c = 55.443	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 6M		2020-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9762	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.37	69.78	99.95	0.15	0.79	2	6.1		13144

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	3.37	3.52			0.1	0.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7ZK1	3.372	69.778	13057	631	92.774	0.251	0.2495	0.25	0.2795	0.28	68.309

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]
-4.757		-2.371	-8.223		12.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.495
r_dihedral_angle_6_deg	17.383
r_dihedral_angle_1_deg	5.72
r_dihedral_angle_2_deg	5.578
r_lrange_it	2.628
r_lrange_other	2.628
r_mcangle_it	2.045
r_mcangle_other	2.045
r_angle_refined_deg	2.006
r_scangle_it	1.814
r_scangle_other	1.814
r_mcbond_it	1.388
r_mcbond_other	1.388
r_scbond_it	1.179
r_scbond_other	1.179
r_angle_other_deg	1.036
r_nbd_other	0.441
r_symmetry_xyhbond_nbd_refined	0.434
r_symmetry_nbd_refined	0.396
r_nbd_refined	0.248
r_symmetry_nbd_other	0.226
r_xyhbond_nbd_refined	0.209
r_nbtor_refined	0.195
r_xyhbond_nbd_other	0.163
r_ncsr_local_group_1	0.149
r_symmetry_xyhbond_nbd_other	0.108
r_ncsr_local_group_2	0.105
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.085
r_bond_other_d	0.044
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5898
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing