8IVX | pdb_00008ivx

Crystal structure of NRP2 in complex with aNRP2-14 Fab fragment

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QQK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	289	30% PEG300, 0.1M Sodium acetate trihydrate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.501	α = 90
b = 89.411	β = 94.18
c = 130.877	γ = 90

Symmetry
Space Group	C 1 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		2019-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97915	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	1.9	50	97.4	0.074	0.082	0.033	0.997	23.28	5.9		78778		-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	1.9	1.93	96.1		0.59	0.649	0.264	0.816	2.41	6.1

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 (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	1.9	46.65	74703	4067	97.13	0.19284	0.191	0.2	0.22547	0.23	RANDOM	45.361

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]
-0.51		-1.04	0.72		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.247
r_long_range_B_refined	7.861
r_long_range_B_other	7.85
r_dihedral_angle_1_deg	6.579
r_scangle_other	6.313
r_scbond_it	4.597
r_scbond_other	4.596
r_mcangle_other	4.217
r_mcangle_it	4.213
r_mcbond_it	3.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.247
r_long_range_B_refined	7.861
r_long_range_B_other	7.85
r_dihedral_angle_1_deg	6.579
r_scangle_other	6.313
r_scbond_it	4.597
r_scbond_other	4.596
r_mcangle_other	4.217
r_mcangle_it	4.213
r_mcbond_it	3.145
r_mcbond_other	3.142
r_angle_refined_deg	1.057
r_angle_other_deg	0.365
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6527
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	4

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.