4S18 | pdb_00004s18

The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and oxaliplatin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	RNase A was crystallized at room temperature mixing 1 L solution of protein at 20 mg mL-1 with an equal volume of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. Two weeks after their appearance, single crystals were soaked for four days in a solution of Oxaliplatin dissolved in 10 L of reservoir. At the final, Pt drugs:protein concentrations were in 10:1 ratio, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.722	α = 90
b = 32.736	β = 90.36
c = 73.233	γ = 90

Symmetry
Space Group	C 1 2 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+	mirrors		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	2.27	50	95.4	0.161		6.6	10764	10764

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1JVT	2.27	50	10237	10237	520	94.27	0.22825	0.22825	0.22451	0.23	0.30092	0.3	RANDOM	46.399

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]
-1.21		0.76	-0.55		1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.39
r_dihedral_angle_3_deg	14.695
r_dihedral_angle_4_deg	10.413
r_long_range_B_refined	7.355
r_long_range_B_other	7.343
r_dihedral_angle_1_deg	6.609
r_mcangle_it	4.941
r_mcangle_other	4.939
r_scangle_other	4.859
r_scbond_it	3.393
r_scbond_other	3.388
r_mcbond_it	3.209
r_mcbond_other	3.206
r_angle_refined_deg	2.53
r_angle_other_deg	1.08
r_chiral_restr	0.091
r_gen_planes_refined	0.033
r_bond_refined_d	0.012
r_bond_other_d	0.004
r_gen_planes_other	0.004
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	1835
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	34

Software

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