8AJ5 | pdb_00008aj5

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

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	20% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.23	α = 90
b = 78.23	β = 90
c = 37.28	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	1.31	55.32	98.9	0.141	0.997	14.3	20		28122

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	1.31	1.33	98.9		1.8	0.755	25.8

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	1.31	55.317	28065	1403	98.779	0.169	0.1676	0.18	0.1976	0.2	18.925

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]
0.037			0.037		-0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.266
r_dihedral_angle_4_deg	20.745
r_dihedral_angle_3_deg	13.831
r_lrange_it	6.649
r_lrange_other	6.648
r_dihedral_angle_1_deg	6.465
r_scangle_it	4.264
r_scangle_other	4.131
r_scbond_it	2.905
r_scbond_other	2.787
r_mcangle_other	2.39
r_mcangle_it	2.389
r_angle_refined_deg	1.839
r_mcbond_it	1.67
r_mcbond_other	1.616
r_angle_other_deg	1.58
r_nbd_refined	0.276
r_nbd_other	0.27
r_xyhbond_nbd_refined	0.236
r_symmetry_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.174
r_symmetry_metal_ion_refined	0.119
r_metal_ion_refined	0.099
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	61

Software

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