8RTJ | pdb_00008rtj

X-ray structure of lysozyme obtained upon reaction with [VIVO(8-HQ)2] in ethylene glycol

X-RAY DIFFRACTION

---

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	4.5	293	20% ethylene glycol, 0.6 M sodium nitrate, 0.1 M sodium acetate at pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2	38.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.14	α = 90
b = 78.14	β = 90
c = 37.52	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		2021-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.00	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.27	55.25	99.9	1	36.5	23.7		31889

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	1.27	1.3			1.629	0.844

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.27	55.236	31030	1532	99.309	0.175	0.1736	0.1804	0.1968	0.2019	23.328

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]
-0.022			-0.022		0.044

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.044
r_dihedral_angle_4_deg	17.161
r_dihedral_angle_3_deg	13.818
r_lrange_it	7.366
r_lrange_other	7.138
r_dihedral_angle_1_deg	6.73
r_scangle_it	5.31
r_scangle_other	5.085
r_scbond_it	3.519
r_scbond_other	3.246
r_mcangle_other	2.647
r_mcangle_it	2.641
r_angle_refined_deg	2.01
r_mcbond_it	1.901
r_mcbond_other	1.871
r_angle_other_deg	1.61
r_nbd_refined	0.234
r_nbd_other	0.217
r_symmetry_nbd_refined	0.204
r_xyhbond_nbd_refined	0.2
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_other	0.197
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.18
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.09
r_metal_ion_refined	0.068
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	52

Software

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