4N0K

Atomic resolution crystal structure of a cytochrome c-calixarene complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TYI	pdb entry 3TYI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293.15	18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.11	α = 90
b = 55.78	β = 90
c = 119.08	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD	Pt coated mirrors	2011-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

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	1.05	15.39	94.9	0.113	9.1	6	113051	107285		2.5	6.2

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	1.05	1.11	100		0.962	1.8	5.4	16317

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3TYI	1.05	15.39	107285	101839	5357	94.82	0.15813	0.15701	0.17976	RANDOM	11.299

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]
-0.43			0.2		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.122
r_sphericity_free	22.839
r_dihedral_angle_4_deg	22.131
r_dihedral_angle_3_deg	11.329
r_sphericity_bonded	6.913
r_dihedral_angle_1_deg	5.868
r_angle_refined_deg	1.266
r_rigid_bond_restr	1.264
r_chiral_restr	0.284
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1692
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	230

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling