5VJO | pdb_00005vjo

Complex between HyHEL10 Fab fragment heavy chain mutant I29F and Pekin duck egg lysozyme isoform I (DEL-I)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5V8G	5V8G, 3D9A
experimental model	PDB	3D9A	5V8G, 3D9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	4.75	293	100 mM sodium citrate (pH 4.75), 17% (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.02	α = 90
b = 102.91	β = 90
c = 133.98	γ = 90

Symmetry
Space Group	P 21 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2016-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	2.43	47.49	99.9	0.095	0.1	0.032	0.998	15.5	9.7		47296

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	2.43	2.51	100		0.77	0.814	0.261	0.85		9.5

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	5V8G, 3D9A	2.43	47.49	44719	2326	99.78	0.2638	0.2621	0.26	0.2959	0.3	RANDOM	58.472

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]
-1.57			2.66		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.813
r_dihedral_angle_4_deg	18.681
r_dihedral_angle_3_deg	14.636
r_dihedral_angle_1_deg	6.815
r_angle_refined_deg	1.439
r_angle_other_deg	0.976
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.813
r_dihedral_angle_4_deg	18.681
r_dihedral_angle_3_deg	14.636
r_dihedral_angle_1_deg	6.815
r_angle_refined_deg	1.439
r_angle_other_deg	0.976
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8170
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	5

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.