6ZS8 | pdb_00006zs8

X-ray structure of the adduct formed upon treating lysozyme with an aged solution of arsenoplatin-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4J1A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	20% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.703	α = 90
b = 78.703	β = 90
c = 34.462	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	CCD	RIGAKU SATURN 944		2015-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	55.65	99.5	0.113	8	5.7		6242

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	100		0.639		5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4J1A	2.153	25.939	6221	289	99.632	0.187	0.1847	0.19	0.2389	0.24	32.612

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]
-0.658			-0.658		1.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.613
r_dihedral_angle_4_deg	20.072
r_dihedral_angle_3_deg	17.939
r_dihedral_angle_1_deg	7.917
r_lrange_it	7.114
r_lrange_other	7.112
r_scangle_it	4.249
r_scangle_other	4.247
r_mcangle_it	3.674
r_mcangle_other	3.672
r_scbond_it	2.724
r_scbond_other	2.722
r_mcbond_other	2.302
r_mcbond_it	2.301
r_angle_refined_deg	1.696
r_angle_other_deg	1.322
r_nbd_other	0.277
r_metal_ion_refined	0.27
r_symmetry_nbd_refined	0.26
r_nbd_refined	0.234
r_symmetry_nbd_other	0.211
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.155
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.071
r_ext_dist_refined_d	0.063
r_xyhbond_nbd_other	0.053
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
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	60
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing