8RTK | pdb_00008rtk

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

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	7.5	293	2.0 M sodium formate, 0.1 M Hepes at pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.08	α = 90
b = 77.08	β = 90
c = 37.53	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 11.2C	1.00	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	1.21	38.543	100	1	27.9	18.5		35157

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	1.21	1.23			0.787

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	1.21	38.543	35053	1734	99.971	0.174	0.1727	0.1792	0.1923	0.1971	19.812

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]
0.01			0.01		-0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.82
r_dihedral_angle_4_deg	18.588
r_dihedral_angle_3_deg	12.942
r_dihedral_angle_1_deg	6.524
r_lrange_it	5.794
r_lrange_other	5.524
r_scangle_other	4.261
r_scangle_it	4.183
r_scbond_it	2.812
r_scbond_other	2.766
r_mcangle_other	2.706
r_mcangle_it	2.691
r_angle_refined_deg	2.193
r_mcbond_it	1.728
r_mcbond_other	1.696
r_angle_other_deg	1.61
r_symmetry_nbd_refined	0.301
r_nbd_refined	0.23
r_nbd_other	0.225
r_xyhbond_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.174
r_chiral_restr	0.114
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.08
r_xyhbond_nbd_other	0.078
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
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	148
Heterogen Atoms	47

Software

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