8AJ3 | pdb_00008aj3

X-ray structure of lysozyme obtained upon reaction with [VIVO(malt)2] (Structure A)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	2.0 M sodium formate and 0.1 M Hepes, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.89	α = 90
b = 76.89	β = 90
c = 38.05	γ = 90

Symmetry
Space Group	P 43 21 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 PILATUS 6M		2021-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.13	54.37	97.3	0.06	0.999	28.4	16.1		42289

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.13	1.15	87.9		0.339	0.926	3.4	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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	193L	1.13	54.369	42156	2091	97.464	0.202	0.1994	0.2	0.2493	0.26	16.146

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]
-0.855			-0.855		1.709

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.195
r_dihedral_angle_4_deg	18.888
r_dihedral_angle_3_deg	13.348
r_dihedral_angle_1_deg	6.497
r_rigid_bond_restr	6.465
r_lrange_it	3.978
r_scangle_it	3.532
r_scbond_it	3.067
r_mcangle_it	2.322
r_mcbond_it	2.014
r_angle_refined_deg	1.883
r_nbtor_refined	0.308
r_symmetry_xyhbond_nbd_refined	0.279
r_metal_ion_refined	0.242
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.202
r_symmetry_nbd_refined	0.184
r_chiral_restr	0.129
r_gen_planes_refined	0.013
r_bond_refined_d	0.012
r_ext_dist_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing