6GDA | pdb_00006gda

Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine

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		293	2.1 M ammonium sulfate 0.1 M MES pH 6.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.252	α = 90
b = 101.252	β = 90
c = 85.31	γ = 90

Symmetry
Space Group	P 43 21 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	PIXEL	DECTRIS EIGER X 9M		2017-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.8	85.31	100	0.123	0.131	0.045	0.997	12.1	8.2		11454

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	100		0.666	0.71	0.243	0.473		8.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YCC	2.8	71.7	10844	570	100	0.223	0.2219	0.2248	0.243	0.2382	RANDOM	68.516

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]
-1.47			-1.47		2.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.912
r_dihedral_angle_3_deg	13.424
r_dihedral_angle_4_deg	10.923
r_dihedral_angle_1_deg	5.189
r_angle_refined_deg	1.192
r_angle_other_deg	0.714
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.912
r_dihedral_angle_3_deg	13.424
r_dihedral_angle_4_deg	10.923
r_dihedral_angle_1_deg	5.189
r_angle_refined_deg	1.192
r_angle_other_deg	0.714
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	846
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	404

Software

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

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.