Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.03848 Å / Relative weight: 1
Reflection
Resolution: 2.21→50 Å / Num. obs: 27498 / % possible obs: 93.9 % / Observed criterion σ(I): 2.2 / Redundancy: 3.6 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.27
Reflection shell
Resolution: 2.21→2.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.39 / % possible all: 64.1
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHASES
phasing
REFMAC
5.6.0031
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: A MONOMER OF HUMAN SYNCAM 3 (NECTIN-LIKE MOLECULE 1) IG1, PROTEIN DATA BANK CODE 1Z9M
Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.049 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.237 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.245
1383
5 %
RANDOM
Rwork
0.198
-
-
-
obs
0.2
26095
94 %
-
all
-
29225
-
-
Solvent computation
Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 45.012 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.96 Å2
-0.42 Å2
1.46 Å2
2-
-
2.52 Å2
-3.35 Å2
3-
-
-
0.77 Å2
Refinement step
Cycle: LAST / Resolution: 2.21→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3099
0
98
192
3389
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
3266
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.234
1.987
4460
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.3
5
392
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.183
25.245
143
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.302
15
532
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.604
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.161
0.2
541
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
2438
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.971
1.5
1977
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.794
2
3225
X-RAY DIFFRACTION
r_scbond_it
3.619
3
1289
X-RAY DIFFRACTION
r_scangle_it
6.023
4.5
1235
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.21→2.27 Å / Total num. of bins used: 20