29OL | pdb_000029ol

X-ray structure of the adduct formed upon reaction of the gold compound AF-Npx with lysozyme (Structure 2)

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	6.5	298	14% PEG 8K, 0.1 M sodium citrate and 0.1 M sodium cacodylate buffer pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.66	α = 90
b = 78.66	β = 90
c = 37.327	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 EIGER X 9M		2025-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.9677	ESRF	ID23-2

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	1.44	39.33	94.4	0.2	0.994	12.9	22.2		20064

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	1.44	1.51	46.7		0.627	21.8	21.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.441	39.33	20047	935	92.2	0.181	0.1796	0.1883	0.1999	0.2032	20.467

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]
-0.081			-0.081		0.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.415
r_dihedral_angle_4_deg	22.08
r_dihedral_angle_3_deg	15.447
r_lrange_it	7.388
r_lrange_other	7.321
r_dihedral_angle_1_deg	6.765
r_scangle_it	5.13
r_scangle_other	5.125
r_scbond_it	3.173
r_scbond_other	3.173
r_mcangle_other	2.819
r_mcangle_it	2.804
r_mcbond_it	1.891
r_mcbond_other	1.855
r_angle_refined_deg	1.812
r_angle_other_deg	1.585
r_symmetry_nbd_refined	0.262
r_xyhbond_nbd_refined	0.235
r_nbd_refined	0.226
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.174
r_nbd_other	0.168
r_symmetry_xyhbond_nbd_refined	0.13
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.087
r_metal_ion_refined	0.024
r_bond_refined_d	0.012
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	79
Heterogen Atoms	5

Software

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