8BPH | pdb_00008bph

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

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

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.19	α = 90
b = 77.19	β = 90
c = 37.83	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	1.00	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	1.07	38.603	96.8	0.042	1	33.8	19.3		949875

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	1.07	1.09			0.809	0.83	2.8

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	1.07	38.603	48803	2421	95.876	0.187	0.1857	0.19	0.2091	0.21	15.021

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		0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.714
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	15.227
r_lrange_it	7.999
r_lrange_other	7.63
r_dihedral_angle_1_deg	6.821
r_scangle_other	3.709
r_scangle_it	3.647
r_scbond_other	2.381
r_scbond_it	2.371
r_angle_refined_deg	2.065
r_mcangle_other	2.064
r_mcangle_it	2.047
r_angle_other_deg	1.686
r_mcbond_it	1.364
r_mcbond_other	1.33
r_nbd_refined	0.274
r_nbd_other	0.248
r_xyhbond_nbd_refined	0.242
r_symmetry_nbd_refined	0.239
r_symmetry_nbd_other	0.224
r_symmetry_xyhbond_nbd_refined	0.219
r_nbtor_refined	0.184
r_chiral_restr	0.121
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	992
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	35

Software

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