9EO2

X-ray structure of the adduct formed upon reaction of picoplatin with lysozyme (structure B)

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	4.5	298	20% ethylene glycol, 0.6 M sodium nitrate and 0.1 sodium acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.57	α = 90
b = 77.57	β = 90
c = 37.64	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		2021-12-04	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	1.36	38.78	100	0.08	0.999	21.3	23.4		25229

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	1.36	1.38	100		2.079	0.782	2.2	24.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.36	38.78	24654	1189	97.562	0.174	0.1728	0.2082	20.421

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]
-0.039			-0.039		0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.277
r_dihedral_angle_4_deg	20.518
r_dihedral_angle_3_deg	15.312
r_lrange_it	6.56
r_dihedral_angle_1_deg	6.523
r_lrange_other	6.331
r_scangle_it	4.691
r_scangle_other	4.688
r_scbond_it	3.112
r_scbond_other	3.109
r_mcangle_other	2.417
r_mcangle_it	2.414
r_angle_refined_deg	1.877
r_mcbond_it	1.759
r_mcbond_other	1.655
r_angle_other_deg	1.611
r_nbd_other	0.348
r_symmetry_nbd_refined	0.267
r_xyhbond_nbd_refined	0.246
r_nbd_refined	0.236
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.104
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_ext_dist_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	36

Software

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