7TNG | pdb_00007tng

Kringle domain of human Receptor Tyrosine Kinase-Like Orphan Receptor 1 (ROR1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BA5	6BA5,6OSN
experimental model	PDB	6OSN	6BA5,6OSN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	0.8-1.2 M Sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.157	α = 90
b = 48.157	β = 90
c = 69.021	γ = 120

Symmetry
Space Group	P 32 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 EIGER X 4M		2018-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	41.71	99.8	0.101	0.063	0.985	18.3	7.4		18755			15.82

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42			0.808	0.494	0.737	1.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6BA5,6OSN	1.4	41.71	17717	1007	99.69	0.21127	0.21113	0.26	0.21394	0.25	RANDOM	18.007

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]
0.19	0.09		0.19		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.839
r_dihedral_angle_4_deg	17.029
r_dihedral_angle_3_deg	11.866
r_dihedral_angle_1_deg	6.845
r_rigid_bond_restr	4.839
r_scangle_other	4.512
r_scbond_it	4.286
r_scbond_other	4.276
r_long_range_B_other	4.074
r_long_range_B_refined	4.067
r_mcangle_it	3.335
r_mcangle_other	3.331
r_mcbond_it	3.096
r_mcbond_other	3.087
r_angle_refined_deg	2.158
r_angle_other_deg	1.644
r_chiral_restr	0.13
r_bond_refined_d	0.018
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	676
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms

Software

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