9JU1 | pdb_00009ju1

Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VPF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	8	277	0.1M Tris-HCl pH 8.0, 0.2M NaCl, 2.5M Ammonium Sulfate, 0.04% NaN3

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.982	α = 90
b = 42.982	β = 90
c = 309.665	γ = 120

Symmetry
Space Group	P 65 2 2

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 16M		2021-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9	SPring-8	BL41XU

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	1.45	44.24	100	0.06	0.061	0.014	0.999	22.3	20.4		31964

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	1.45	1.47		100	0.786	0.807	0.183	0.92		19.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.45	37.251	31791	1533	99.981	0.217	0.2156	0.2225	0.2449	0.251	RANDOM	27.699

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]
0.497	0.248		0.497		-1.611

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.517
r_dihedral_angle_6_deg	14.071
r_dihedral_angle_2_deg	9.013
r_lrange_it	8.907
r_lrange_other	8.866
r_scangle_it	7.197
r_scangle_other	7.193
r_dihedral_angle_1_deg	5.764
r_scbond_it	4.637
r_scbond_other	4.633
r_mcangle_other	4.175
r_mcangle_it	4.174
r_mcbond_it	2.854
r_mcbond_other	2.846
r_angle_refined_deg	1.919
r_angle_other_deg	0.627
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_refined	0.207
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.155
r_nbd_other	0.155
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1117
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	5

Software

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