29LJ | pdb_000029lj

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-CNPhF)(O2CCH3)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	4	293	20% ethylene glycol, 0.1 M sodium acetate at pH 4.0, and 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.18	α = 90
b = 78.18	β = 90
c = 37.53	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		2022-07-16	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	1.13	55.28	86.94	0.042	1	21.8	9.9		38424

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	1.13	1.15			0.836	0.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.13	55.28	38424	1837	86.94	0.199	0.1982	0.205	0.2095	0.2155	RANDOM	20.479

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]
-0.078			-0.078		0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.243
r_dihedral_angle_6_deg	13.94
r_lrange_it	7.783
r_lrange_other	7.521
r_dihedral_angle_1_deg	6.278
r_dihedral_angle_2_deg	5.297
r_scangle_other	4.673
r_scangle_it	4.5
r_scbond_other	3.086
r_scbond_it	2.986
r_mcangle_it	2.846
r_mcangle_other	2.844
r_angle_refined_deg	1.993
r_mcbond_it	1.969
r_mcbond_other	1.945
r_angle_other_deg	0.69
r_symmetry_nbd_refined	0.272
r_nbd_refined	0.25
r_symmetry_nbd_other	0.197
r_nbd_other	0.192
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.153
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.082
r_metal_ion_refined	0.069
r_bond_refined_d	0.012
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	127
Heterogen Atoms	81

Software

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