8IVW

Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	289	21% PEG1000, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 0.05M Lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.424	α = 90
b = 225.164	β = 91.3
c = 142.996	γ = 90

Symmetry
Space Group	P 1 21 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		2021-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	3.2	50	90.9	0.274	0.298	0.116	0.957	4.33	6.3		66035		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.26	89.3		1.247	1.352	0.517	0.434	1	6.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.205	49.65	62689	3309	90.56	0.25	0.2477	0.2941	87.439

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]
-1.018		-0.975	1.911		-0.848

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	24.159
r_lrange_it	18.386
r_lrange_other	18.386
r_dihedral_angle_6_deg	17.832
r_mcangle_other	10.371
r_mcangle_it	10.37
r_scangle_it	9.588
r_scangle_other	9.588
r_dihedral_angle_1_deg	6.879
r_mcbond_it	6.311
r_mcbond_other	6.31
r_dihedral_angle_2_deg	5.769
r_scbond_it	5.715
r_scbond_other	5.715
r_angle_refined_deg	1.313
r_angle_other_deg	0.477
r_symmetry_nbd_refined	0.334
r_nbd_other	0.316
r_xyhbond_nbd_refined	0.233
r_symmetry_nbd_other	0.222
r_nbd_refined	0.207
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_other	0.165
r_ncsr_local_group_10	0.131
r_ncsr_local_group_16	0.126
r_ncsr_local_group_2	0.123
r_ncsr_local_group_1	0.112
r_ncsr_local_group_3	0.11
r_ncsr_local_group_11	0.103
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.062
r_ext_dist_refined_b	0.049
r_ncsr_local_group_4	0.029
r_ncsr_local_group_6	0.028
r_ncsr_local_group_12	0.027
r_ncsr_local_group_17	0.026
r_ncsr_local_group_5	0.02
r_ncsr_local_group_14	0.017
r_ncsr_local_group_7	0.016
r_ncsr_local_group_15	0.016
r_ncsr_local_group_13	0.013
r_ncsr_local_group_18	0.011
r_ncsr_local_group_9	0.01
r_ncsr_local_group_8	0.009
r_bond_refined_d	0.006
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	26621
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing