9ENZ | pdb_00009enz

X-ray structure of the adduct formed upon reaction of picoplatin with lysozyme (structure 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	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
1.99	38.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.4	α = 90
b = 78.4	β = 90
c = 37.15	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	1.6	39.203	99.6	0.07	0.999	25.3	21.6		15767

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	1.6	1.63	99.3		1.2532	0.887	3.2	23.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	39.203	15625	790	98.824	0.186	0.1832	0.19	0.2298	0.24	26.483

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]
-0.162			-0.162		0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.204
r_dihedral_angle_4_deg	24.442
r_dihedral_angle_3_deg	12.986
r_lrange_it	7.047
r_lrange_other	7.005
r_dihedral_angle_1_deg	6.982
r_scangle_it	5.408
r_scangle_other	5.395
r_scbond_it	3.416
r_scbond_other	3.415
r_mcangle_it	3.159
r_mcangle_other	3.137
r_mcbond_it	2.376
r_mcbond_other	2.313
r_angle_refined_deg	1.699
r_angle_other_deg	1.501
r_symmetry_xyhbond_nbd_refined	0.307
r_symmetry_nbd_refined	0.226
r_nbd_other	0.224
r_xyhbond_nbd_refined	0.222
r_nbd_refined	0.22
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.165
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_ext_dist_refined_d	0.004
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	106
Heterogen Atoms	21

Software

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