7QVK

NM-02 in complex with HER2-ECD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	13% PEG6000 (w/v), 0.1 M MES pH 6.5, 7% 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
3.578768	65.65199

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.767	α = 90
b = 105.767	β = 90
c = 185.882	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 PILATUS3 6M		2019-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96872	Diamond	I24

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	3.1	65.324	100	0.99	5.1	19.2		22490			101.26

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	3.1	3.31	100		0.34	0.7	19.7

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5MY6	3.1	65.324	22447	1186	99.858	0.278	0.2747	0.2751	0.3299	Random selection	105.683

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]
-3.441	-1.721		-3.441		11.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.735
r_dihedral_angle_3_deg	17.891
r_dihedral_angle_4_deg	12.787
r_lrange_it	11.966
r_lrange_other	11.966
r_mcangle_it	8.358
r_mcangle_other	8.357
r_scangle_it	7.346
r_scangle_other	7.345
r_dihedral_angle_1_deg	6.404
r_mcbond_other	5.053
r_mcbond_it	5.052
r_scbond_it	4.345
r_scbond_other	4.345
r_angle_other_deg	2.586
r_angle_refined_deg	1.406
r_symmetry_xyhbond_nbd_refined	0.586
r_symmetry_nbd_other	0.251
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.193
r_nbd_other	0.192
r_nbtor_refined	0.161
r_xyhbond_nbd_other	0.142
r_symmetry_nbd_refined	0.107
r_symmetry_xyhbond_nbd_other	0.082
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.05
r_bond_other_d	0.036
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4783
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	53

Software

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