8PH8 | pdb_00008ph8

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DPhF)2(O2CCH3)2] 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	7	293	0.8 M succinic acid at pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.89	α = 90
b = 76.89	β = 90
c = 37.89	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	1.29	54.37	99.7	0.074	0.999	21.2	20.8		37185

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	1.29	1.31			1.14	0.763	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	1.29	54.336	29187	1446	99.955	0.158	0.1563	0.17	0.1873	0.19	18.008

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]
-0.059			-0.059		0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.328
r_dihedral_angle_4_deg	23.915
r_dihedral_angle_3_deg	11.623
r_dihedral_angle_1_deg	6.626
r_lrange_it	5.661
r_lrange_other	5.179
r_scangle_it	3.468
r_scangle_other	3.466
r_scbond_other	2.248
r_scbond_it	2.247
r_mcangle_other	2.203
r_mcangle_it	2.176
r_angle_refined_deg	1.922
r_angle_other_deg	1.642
r_mcbond_it	1.458
r_mcbond_other	1.391
r_symmetry_nbd_refined	0.272
r_xyhbond_nbd_refined	0.264
r_nbd_other	0.233
r_nbd_refined	0.227
r_nbtor_refined	0.189
r_symmetry_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.112
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.085
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	177
Heterogen Atoms	99

Software

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