8PH7 | pdb_00008ph7

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DPhF)(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	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 = 77.67	α = 90
b = 77.67	β = 90
c = 38.28	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	1.406	54.921	99.4	0.164	0.998	13.3	19.3		14799

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	1.406	1.53			2.764	0.867	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	1.406	54.921	14799	742	63.385	0.229	0.2264	0.23	0.2664	0.28	24.732

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]
-0.295			-0.295		0.589

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.923
r_dihedral_angle_6_deg	15.551
r_lrange_it	8.612
r_lrange_other	8.585
r_dihedral_angle_2_deg	8.498
r_dihedral_angle_1_deg	7.113
r_scangle_it	4.998
r_scangle_other	4.995
r_mcangle_other	3.467
r_mcangle_it	3.464
r_scbond_it	3.067
r_scbond_other	3.067
r_mcbond_it	2.25
r_mcbond_other	2.247
r_angle_refined_deg	1.631
r_angle_other_deg	0.569
r_nbd_refined	0.242
r_xyhbond_nbd_refined	0.201
r_symmetry_nbd_refined	0.201
r_symmetry_nbd_other	0.195
r_symmetry_xyhbond_nbd_refined	0.191
r_nbd_other	0.177
r_nbtor_refined	0.166
r_metal_ion_refined	0.103
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1000
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	67

Software

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