6LDG

Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96I AB5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IQ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	25% PEG 3350, 100 mM HEPES pH 7.5, 200 mM sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.723	α = 90
b = 53.723	β = 90
c = 250.757	γ = 120

Symmetry
Space Group	P 61 2 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	ADSC QUANTUM 270		2019-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.987	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.98	28.38	99.8	0.129	105.8	40		15931

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.01	100		0.323		40.2

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	3IQ6	1.98	28.38	14722	769	99.79	0.1706	0.1679	0.2213	RANDOM	22.766

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]
0.15	0.08		0.15		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.476
r_dihedral_angle_3_deg	15.292
r_dihedral_angle_4_deg	5.691
r_dihedral_angle_1_deg	5.32
r_angle_refined_deg	1.709
r_angle_other_deg	1.465
r_chiral_restr	0.081
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.476
r_dihedral_angle_3_deg	15.292
r_dihedral_angle_4_deg	5.691
r_dihedral_angle_1_deg	5.32
r_angle_refined_deg	1.709
r_angle_other_deg	1.465
r_chiral_restr	0.081
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1658
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	97

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
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.