8PFW | pdb_00008pfw

X-ray structure of the adduct formed upon reaction of Lysozyme with K2[Ru2(DAniF)(CO3)3] in condition 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	4.5	293	20% ethylene glycol, 0.6 M NaNO3, 0.1 M NaOAc pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.81	α = 90
b = 77.81	β = 90
c = 37.39	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		2022-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1	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	1.12	55.02	99.9	0.054	0.999	27.2	11		44515

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	1.12	1.14			1.324	0.807	2.2

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	1.12	55.02	44515	2291	99.624	0.203	0.2012	0.2063	0.2394	0.2461	17.804

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]
-0.043			-0.043		0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.296
r_dihedral_angle_6_deg	15.938
r_dihedral_angle_2_deg	7.246
r_dihedral_angle_1_deg	6.687
r_lrange_it	4.948
r_lrange_other	4.891
r_scangle_other	3.725
r_angle_refined_deg	3.691
r_scangle_it	3.501
r_scbond_other	2.362
r_mcangle_other	2.349
r_mcangle_it	2.329
r_scbond_it	2.273
r_mcbond_it	1.69
r_mcbond_other	1.69
r_angle_other_deg	0.623
r_nbd_refined	0.241
r_symmetry_nbd_refined	0.207
r_symmetry_nbd_other	0.199
r_nbd_other	0.195
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.123
r_chiral_restr	0.096
r_metal_ion_refined	0.092
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.011
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	87
Heterogen Atoms	109

Software

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