7DCL | pdb_00007dcl

Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96I/A38S AB5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QI5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	21% Polyethylene glycol (PEG) 400, bis-tris, ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.408	α = 90
b = 53.408	β = 90
c = 251.61	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	PIXEL	DECTRIS PILATUS3 6M		2020-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.979	PAL/PLS	11C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.45	46.55	99.9	0.118	0.12	0.021	88.55	34.2		14826

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	2.45	2.49	100		0.177	0.18	0.029	0.994		37.3

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	3QI5	2.45	45.53	8155	420	99.94	0.2001	0.1973	0.2	0.2563	0.26	RANDOM	37.945

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]
-0.25	-0.12		-0.25		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.208
r_dihedral_angle_3_deg	15.92
r_dihedral_angle_1_deg	5.001
r_dihedral_angle_4_deg	4.641
r_angle_refined_deg	1.352
r_angle_other_deg	1.215
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.208
r_dihedral_angle_3_deg	15.92
r_dihedral_angle_1_deg	5.001
r_dihedral_angle_4_deg	4.641
r_angle_refined_deg	1.352
r_angle_other_deg	1.215
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1660
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	95

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.