6ZSR | pdb_00006zsr

Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 72 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
2.14	42.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.62	α = 70.27
b = 48.8	β = 68.49
c = 49.18	γ = 76.99

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		2020-03-16	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	43.91	86	0.077	0.996	10.2	3.4		17566

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	83.7		0.235	0.89	3.7

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	2.005	23.295	15643	782	76.633	0.203	0.1984	0.2	0.2834	0.29	22.458

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]
-0.244	-0.094	0.692	0.809	1.641	0.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.642
r_dihedral_angle_3_deg	16.986
r_dihedral_angle_4_deg	15.134
r_dihedral_angle_1_deg	7.776
r_lrange_it	6.764
r_lrange_other	6.74
r_scangle_it	3.388
r_scangle_other	3.332
r_mcangle_it	3.286
r_mcangle_other	3.285
r_scbond_it	2.062
r_scbond_other	2.032
r_mcbond_it	1.989
r_mcbond_other	1.987
r_angle_refined_deg	1.557
r_angle_other_deg	1.234
r_symmetry_nbd_refined	0.237
r_nbd_other	0.22
r_ext_dist_refined_d	0.211
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.197
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.153
r_ncsr_local_group_1	0.144
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2556
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	17

Software

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