6GD6 | pdb_00006gd6

Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with ammonium sulfate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LYC	5LYC chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	1.75 M ammonium sulfate 0.2 M NaCl (2x protein solution : 1x crystallisation condition)

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.003	α = 90
b = 82.003	β = 90
c = 82.535	γ = 120

Symmetry
Space Group	H 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	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	1.2	35.68	99.8	0.055	0.064	0.032	0.998	9.9	3.7		64600

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	1.2	1.22	99.5		0.533	0.636	0.341	0.735		3.3

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	5LYC chain A	1.2	35.68	61332	3238	99.76	0.1197	0.1189	0.13	0.1361	0.14	RANDOM	18.231

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]
0.08	0.04		0.08		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.406
r_sphericity_free	24.714
r_dihedral_angle_4_deg	17.414
r_dihedral_angle_3_deg	11.771
r_sphericity_bonded	8.366
r_dihedral_angle_1_deg	6.461
r_angle_refined_deg	1.48
r_rigid_bond_restr	0.961
r_angle_other_deg	0.873
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.406
r_sphericity_free	24.714
r_dihedral_angle_4_deg	17.414
r_dihedral_angle_3_deg	11.771
r_sphericity_bonded	8.366
r_dihedral_angle_1_deg	6.461
r_angle_refined_deg	1.48
r_rigid_bond_restr	0.961
r_angle_other_deg	0.873
r_chiral_restr	0.096
r_gen_planes_refined	0.013
r_gen_planes_other	0.013
r_bond_refined_d	0.011
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	846
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	164

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.