29MN | pdb_000029mn

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(p-TolA)(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	38.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.12	α = 90
b = 78.12	β = 90
c = 37.58	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)	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	1.31	55.24	99.6	1	27	12.9		30924

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.33			0.806

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	1.311	55.239	26987	1382	99.6	0.184	0.183	0.1875	0.194	0.1981	RANDOM	21.819

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]
-0.493			-0.493		0.985

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.968
r_dihedral_angle_3_deg	14.427
r_dihedral_angle_2_deg	8.146
r_lrange_it	6.678
r_lrange_other	6.579
r_dihedral_angle_1_deg	6.384
r_scangle_it	5.021
r_scangle_other	4.999
r_scbond_it	3.359
r_scbond_other	3.304
r_mcangle_other	2.871
r_mcangle_it	2.856
r_angle_refined_deg	1.985
r_mcbond_it	1.971
r_mcbond_other	1.93
r_angle_other_deg	0.694
r_symmetry_nbd_refined	0.264
r_nbd_refined	0.247
r_symmetry_xyhbond_nbd_refined	0.243
r_symmetry_nbd_other	0.2
r_nbd_other	0.188
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.06
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
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	46

Software

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