4S1Y | pdb_00004s1y

X-ray structure of human serum albumin complexed with cisplatin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HK1	PDB code 1HK1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	298	Crystals of a cisplatin/HSA adduct were obtained by soaking: more in detail, crystals of defatted HSA, grown after four weeks by sitting drop vapour diffusion method at 25 C using a reservoir solution of 30 % w/v polyethylene glycol 3350 in 50 mM potassium phosphate at pH 7.4 and protein concentration of 30 mg mL-1 (see experimental section or further details), were soaked for 24 h in a 0.005 M cisplatin solution in the same reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.789	α = 90
b = 86.474	β = 103.7
c = 59.141	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	3.16	57.46	96.4	0.149		2.5	9393	9393

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 1HK1	3.16	57.46	8934	449	96.22	0.22781	0.22781	0.22311	0.22	0.32943	0.33	RANDOM	49.033

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]
2.23		0.72	-0.98		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.947
r_dihedral_angle_4_deg	19.571
r_dihedral_angle_3_deg	16.433
r_long_range_B_refined	7.722
r_long_range_B_other	7.722
r_dihedral_angle_1_deg	5.907
r_mcangle_it	4.733
r_mcangle_other	4.733
r_scangle_other	4.639
r_mcbond_it	2.84
r_mcbond_other	2.833
r_scbond_it	2.81
r_scbond_other	2.81
r_angle_refined_deg	1.384
r_angle_other_deg	0.829
r_chiral_restr	0.07
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4195
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	11

Software

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