4S0Q | pdb_00004s0q

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

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, chain A without water molecules and ligands

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	Crystals of the RNase A-carboplatin adduct have been obtained by soaking experiments where pre-grown monoclinic protein crystals were incubated with an excess of the platinum drug (at a protein to platinum ratio 1:10). Crystals of RNase A were grown by hanging-drop vapor mixing 1 L of RNase A at 20 mg mL-1 with equal volumes of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0 at 298 K. Two weeks after their appearance, crystals were soaked for four days in a solution of Carboplatin dissolved in 10 L of reservoir. At the final, Pt drug:protein concentrations were in 10:1 ratio., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.521	α = 90
b = 32.499	β = 89.59
c = 72.711	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					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	2.09	72.71	99.7	0.124		5.6	14095	14095

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, chain A without water molecules and ligands	2.09	72.71	13380	13380	709	99.02	0.20801	0.20801	0.20518	0.21	0.26175	0.27	RANDOM	37.837

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]
-1.17		-0.16	0.48		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.511
r_dihedral_angle_3_deg	15.188
r_dihedral_angle_4_deg	10.612
r_dihedral_angle_1_deg	6.895
r_long_range_B_refined	6.465
r_long_range_B_other	6.454
r_scangle_other	4.656
r_mcangle_it	3.991
r_mcangle_other	3.99
r_scbond_it	3.219
r_scbond_other	3.219
r_mcbond_it	2.744
r_mcbond_other	2.744
r_angle_refined_deg	1.762
r_angle_other_deg	0.846
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
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	1844
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement