9RK6 | pdb_00009rk6

Paraplegin N-terminal domain

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		289	10mM NaCitrate, 15% Peg8k with seeds from 0.17M Ammonium sulfate, 25.5% PEG 4K, 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.393	α = 90
b = 63.844	β = 90
c = 99.813	γ = 90

Symmetry
Space Group	C 2 2 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		2019-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979515	Diamond	I04

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	1.99	49.96	99.89	0.999	11.7	7.2		12698			42.56

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	1.99	2.01	62.9		0.664		8.3

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	1.99	49.956	12698	170	99.89	0.24	0.2386	0.239	0.2961	0.2608	64.309

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]
0.253			-0.309		0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	16.94
r_lrange_it	16.932
r_dihedral_angle_6_deg	15.109
r_dihedral_angle_3_deg	14.288
r_scangle_it	8.146
r_scangle_other	8.145
r_mcangle_it	6.516
r_mcangle_other	6.512
r_dihedral_angle_1_deg	6.459
r_scbond_it	5.143
r_scbond_other	5.141
r_mcbond_it	4.487
r_mcbond_other	4.487
r_dihedral_angle_2_deg	4.08
r_angle_refined_deg	1.455
r_angle_other_deg	0.493
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.24
r_symmetry_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.19
r_nbd_other	0.163
r_symmetry_nbd_refined	0.162
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.062
r_symmetry_xyhbond_nbd_other	0.021
r_xyhbond_nbd_other	0.012
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1365
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing