Experiment: 5NCV

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	20 % PEG 8000, 50 mM NaCl, 50 mM sodium acetate (pH 5.6). [Cytochrome c] = 0.75 mM and [Methylphosphonatocalix[4]arene] = 0.3 mM

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.917	α = 90
b = 80.227	β = 93.07
c = 47.807	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M-F		2016-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.979	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.5	47.74	99.2	0.055	0.026	0.999	18.7	5.5		34591

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	99.4		0.055	0.158	5.1	5.4

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	1YCC	1.5	47.74	32897	1707	99.23	0.1719	0.1704	0.2012	RANDOM	20.624

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]
0.3		-2.11	-0.88		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.978
r_dihedral_angle_4_deg	24.671
r_dihedral_angle_3_deg	14.117
r_dihedral_angle_1_deg	6.26
r_angle_refined_deg	1.608
r_angle_other_deg	1.012
r_chiral_restr	0.122
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_gen_planes_other	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.978
r_dihedral_angle_4_deg	24.671
r_dihedral_angle_3_deg	14.117
r_dihedral_angle_1_deg	6.26
r_angle_refined_deg	1.608
r_angle_other_deg	1.012
r_chiral_restr	0.122
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_gen_planes_other	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1624
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	295

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.