8BPJ | pdb_00008bpj

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-FPhF)(O2CCH3)3] (Structure 1)

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	293	20% ethylene glycol, 0.1 M sodium acetate buffer at pH 4.0, 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.48	α = 90
b = 77.48	β = 90
c = 37.27	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	1.38	54.79	99.9	0.047	0.99	21.8	10.3		23817

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	1.38	1.4			0.935	0.833	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	193L	1.38	54.79	23817	1197	99.933	0.192	0.1901	0.2	0.2306	0.24	24.069

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]
-0.049			-0.049		0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.303
r_dihedral_angle_4_deg	20.462
r_dihedral_angle_3_deg	16.08
r_dihedral_angle_1_deg	6.64
r_lrange_it	6.341
r_lrange_other	6.27
r_scangle_it	4.813
r_scangle_other	4.795
r_scbond_it	3.194
r_scbond_other	3.14
r_mcangle_it	2.908
r_mcangle_other	2.908
r_mcbond_it	2.079
r_mcbond_other	2.075
r_angle_refined_deg	1.921
r_angle_other_deg	1.577
r_symmetry_xyhbond_nbd_refined	0.258
r_nbd_refined	0.234
r_nbd_other	0.227
r_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.198
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_other	0.154
r_metal_ion_refined	0.136
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.013
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	109
Heterogen Atoms	71

Software

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