8OM8 | pdb_00008om8

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

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	293	1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.06	α = 90
b = 78.06	β = 90
c = 37.01	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		2022-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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	1.08	55.4	100	1	33.2	20		50384

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.08	1.1			0.744

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	1.08	55.258	45671	2314	92.194	0.15	0.1476	0.15	0.1895	0.2	20.124

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]
1.684			1.684		-3.369

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.163
r_dihedral_angle_4_deg	17.774
r_rigid_bond_restr	14.495
r_dihedral_angle_3_deg	12.752
r_dihedral_angle_1_deg	6.421
r_scangle_it	5.64
r_scangle_other	5.606
r_scbond_other	5.374
r_scbond_it	5.359
r_lrange_it	4.65
r_lrange_other	4.27
r_angle_refined_deg	2.967
r_mcangle_other	2.436
r_mcangle_it	2.422
r_mcbond_it	2.361
r_mcbond_other	2.322
r_angle_other_deg	1.71
r_nbd_refined	0.343
r_symmetry_nbd_other	0.257
r_nbd_other	0.257
r_xyhbond_nbd_refined	0.225
r_symmetry_nbd_refined	0.204
r_symmetry_xyhbond_nbd_other	0.201
r_nbtor_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.167
r_chiral_restr	0.141
r_symmetry_nbtor_other	0.089
r_metal_ion_refined	0.042
r_bond_refined_d	0.022
r_gen_planes_refined	0.014
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	66

Software

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