4U3X

Structure of a human VH antibody domain binding to the cleft of hen egg lysozyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LYZ	1LYZ, 1OHQ
experimental model	PDB	1OHQ	1LYZ, 1OHQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	300 mM sodium citrate, 16% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.07	α = 90
b = 39.24	β = 104.16
c = 100.18	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	CCD	ADSC QUANTUM 315r		2014-04-12	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)	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	2.26	97.14	98.6	2.4	1.5		24456

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1LYZ, 1OHQ	2.26	97.14	22746	1252	98.12	0.1923	0.1893	0.24839	RANDOM	14.923

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]
0.87		0.35	-0.38		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.824
r_dihedral_angle_4_deg	24.604
r_dihedral_angle_3_deg	13.985
r_dihedral_angle_1_deg	7.248
r_long_range_B_refined	3.332
r_long_range_B_other	3.325
r_scangle_other	1.75
r_angle_refined_deg	1.709
r_mcangle_it	1.594
r_mcangle_other	1.594
r_scbond_it	1.159
r_scbond_other	1.159
r_mcbond_it	0.962
r_mcbond_other	0.949
r_angle_other_deg	0.906
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3576
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement