8PFV | pdb_00008pfv

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DAniF)(O2CCH3)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 = 78.35	α = 90
b = 78.35	β = 90
c = 37.64	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		2022-06-17	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	1.46	55.402	99.9	0.047	1	23.7	10.3		21101

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	1.46	1.48			0.997	0.762	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	1.46	55.402	20914	1067	99.928	0.181	0.1795	0.19	0.2111	0.21	23.591

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]
0.018			0.018		-0.037

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.045
r_dihedral_angle_4_deg	22.886
r_dihedral_angle_3_deg	14.715
r_dihedral_angle_1_deg	6.817
r_lrange_it	6.002
r_lrange_other	5.994
r_scangle_it	5.019
r_scangle_other	4.991
r_scbond_it	3.448
r_scbond_other	3.276
r_mcangle_other	2.823
r_mcangle_it	2.822
r_mcbond_it	2.014
r_mcbond_other	2.003
r_angle_refined_deg	1.996
r_angle_other_deg	1.684
r_nbd_refined	0.243
r_nbd_other	0.208
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.191
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_other	0.121
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.085
r_metal_ion_refined	0.064
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
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	78
Heterogen Atoms	51

Software

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