8PFX | pdb_00008pfx

X-ray structure of the adduct formed upon reaction of Lysozyme with K2[Ru2(D-p-FPhF)(CO3)3] in condition 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	7.5	293	2 M sodium formate and 0.1 M Hepes, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.72	α = 90
b = 76.72	β = 90
c = 38.39	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		2022-06-13	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	1.03	38.36	100	0.034	1	33.7	11.4		57486

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	1.03	1.04			0.753	0.858	2.3

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	1.03	38.36	55049	2721	96.391	0.193	0.192	0.2009	0.2144	0.22	12.285

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]
-0.025			-0.025		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.482
r_dihedral_angle_3_deg	12.733
r_dihedral_angle_2_deg	10.403
r_dihedral_angle_1_deg	5.993
r_lrange_it	5.31
r_lrange_other	4.991
r_scangle_other	3.714
r_scangle_it	3.638
r_scbond_it	2.397
r_scbond_other	2.317
r_angle_refined_deg	1.933
r_mcangle_other	1.742
r_mcangle_it	1.735
r_mcbond_it	1.202
r_mcbond_other	1.201
r_angle_other_deg	0.635
r_symmetry_xyhbond_nbd_refined	0.295
r_nbd_refined	0.249
r_nbd_other	0.206
r_symmetry_nbd_other	0.204
r_xyhbond_nbd_refined	0.198
r_nbtor_refined	0.186
r_symmetry_nbd_refined	0.185
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.081
r_xyhbond_nbd_other	0.079
r_metal_ion_refined	0.061
r_symmetry_xyhbond_nbd_other	0.03
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	137
Heterogen Atoms	51

Software

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