6ZSQ | pdb_00006zsq

Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 18 h of soaking

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BEB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	293	Crystals of beta-Lactoglobulin were grown using 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer pH 6.9 as reservoir. Protein crystallizes at a concentration of 18 mg/mL. Crystals of beta-Lactoglobulin were soaked in a solution consisting of 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer (pH 6.9) with 5 mM CDDP (about 1:3 protein to metal ratio).

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.72	α = 69.96
b = 49.05	β = 68.59
c = 49.31	γ = 77

Symmetry
Space Group	P 1

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		2018-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	2	23.23	86.9	0.06	0.958	8.8	2.3		17918

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	2	2.06	92.4		0.152	0.939	3.9	1.9

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	1BEB	2.004	23.228	17918	894	86.874	0.185	0.1827	0.19	0.2241	0.23	22.264

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]
0.233	0.286	0.182	-0.056	1.707	0.611

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.838
r_dihedral_angle_3_deg	18.598
r_dihedral_angle_4_deg	16.465
r_lrange_it	9.099
r_lrange_other	9.093
r_dihedral_angle_1_deg	6.959
r_scangle_it	4.046
r_scangle_other	3.99
r_mcangle_other	3.522
r_mcangle_it	3.521
r_scbond_it	2.469
r_scbond_other	2.439
r_mcbond_it	2.093
r_mcbond_other	2.092
r_angle_refined_deg	1.616
r_angle_other_deg	1.246
r_ext_dist_refined_d	0.3
r_nbd_other	0.218
r_nbd_refined	0.205
r_symmetry_nbd_other	0.202
r_xyhbond_nbd_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.154
r_symmetry_nbd_refined	0.136
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.008
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	2556
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing