29MY | pdb_000029my

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-o-TolF)(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
1.97	37.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.69	α = 90
b = 77.69	β = 90
c = 37.51	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		2022-09-29	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	1.747	38.88	99.4	0.993	9.7	21.8		12107

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	1.747	1.77			0.805

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	1.747	38.843	11491	586	99.416	0.224	0.2221	0.2255	0.2526	0.2613	RANDOM	34.078

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]
-0.328			-0.328		0.655

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.326
r_dihedral_angle_6_deg	13.669
r_lrange_other	8.281
r_lrange_it	8.208
r_dihedral_angle_2_deg	6.911
r_dihedral_angle_1_deg	6.839
r_scangle_it	5.907
r_scangle_other	5.644
r_scbond_it	4.023
r_mcangle_other	3.943
r_mcangle_it	3.925
r_scbond_other	3.688
r_mcbond_it	2.927
r_mcbond_other	2.917
r_angle_refined_deg	1.677
r_angle_other_deg	0.608
r_nbd_refined	0.245
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_other	0.203
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.174
r_metal_ion_refined	0.172
r_nbd_other	0.136
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.007
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	1001
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	69

Software

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