4RSZ | pdb_00004rsz

The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	300	A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.344	α = 90
b = 120.344	β = 90
c = 36.673	γ = 120

Symmetry
Space Group	P 3

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	2014-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	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	2.19	104.22	99.8	0.109		10.4	30538	30538

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 1HRC	2.19	104.22	28987	28987	1544	99.79	0.23403	0.23403	0.23144	0.24	0.28211	0.28	RANDOM	48.561

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]
-0.8	-0.4		-0.8		2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.76
r_dihedral_angle_4_deg	28.912
r_dihedral_angle_3_deg	17.446
r_long_range_B_refined	5.884
r_dihedral_angle_1_deg	5.865
r_long_range_B_other	5.848
r_scangle_other	3.102
r_mcangle_it	2.688
r_mcangle_other	2.687
r_scbond_it	2.276
r_scbond_other	2.227
r_angle_refined_deg	1.845
r_mcbond_it	1.629
r_mcbond_other	1.629
r_angle_other_deg	1.431
r_chiral_restr	0.106
r_gen_planes_other	0.024
r_gen_planes_refined	0.017
r_bond_refined_d	0.015
r_bond_other_d	0.008
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	4938
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	347

Software

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