6YJD | pdb_00006yjd

Lamin A coil2 dimer stabilized by N-terminal capping

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	277	35% (v/v) methanol, 0.2 M MgCl2 and 0.1 M HEPES

Crystal Properties
Matthews coefficient	Solvent content
6.21	80.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.25	α = 90
b = 117.25	β = 90
c = 93.156	γ = 120

Symmetry
Space Group	P 61 2 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 EIGER X 16M		2019-02-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978565	SOLEIL	PROXIMA 1

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	2.9	44.62	98.28	0.999	20.27	19.2		8792			110.62

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	2.9	3			0.934	0.99

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	SAD	FREE R-VALUE	2.9	44.62	8791	841	99.75	0.258	0.2533	0.26	0.3042	0.3	115.019

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]
3.572	1.786		3.572		-11.586

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.964
r_dihedral_angle_3_deg	19.741
r_lrange_other	19.466
r_lrange_it	19.464
r_scangle_it	19.42
r_scangle_other	19.405
r_dihedral_angle_4_deg	15.216
r_scbond_it	14.654
r_scbond_other	14.64
r_mcangle_it	12.29
r_mcangle_other	12.279
r_mcbond_it	9.868
r_mcbond_other	9.838
r_dihedral_angle_1_deg	4.23
r_angle_refined_deg	1.761
r_angle_other_deg	1.391
r_nbd_other	0.33
r_nbd_refined	0.233
r_symmetry_xyhbond_nbd_refined	0.217
r_symmetry_nbd_refined	0.197
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.158
r_nbtor_refined	0.155
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.084
r_nbtor_other	0.02
r_bond_refined_d	0.01
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	823
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Auto-Rickshaw	phasing