5MIK

X-ray structure of carboplatin-encapsulated horse spleen apoferritin (rotating anode data)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	298	0.8 M (NH4)2SO4, 0.1 M Tris pH 7.7, 60 mM CdSO4.

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.654	α = 90
b = 180.654	β = 90
c = 180.654	γ = 90

Symmetry
Space Group	F 4 3 2

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	2015-11-10	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	1.96	104.3	99.9	0.107	6.2	6.9		18700

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	2	100		0.489	3.8	5.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5erk	1.96	104.3	17792	904	99.88	0.14847	0.14623	0.19161	RANDOM	20.803

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.81
r_dihedral_angle_4_deg	24.43
r_dihedral_angle_3_deg	14.998
r_long_range_B_refined	7.612
r_long_range_B_other	7.61
r_dihedral_angle_1_deg	5.637
r_scangle_other	4.523
r_scbond_it	2.887
r_scbond_other	2.872
r_mcangle_it	2.762
r_mcangle_other	2.76
r_mcbond_it	1.87
r_mcbond_other	1.866
r_angle_refined_deg	1.729
r_angle_other_deg	1.028
r_chiral_restr	0.111
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002
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	1386
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	33

Software

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