Experiment: 9V62

Cryogenic temprature crystal structure of Escherichia coli CyaY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EW4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	4 M NaCl, 0.1 M citric acid, pH:4

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.486	α = 90
b = 44.486	β = 90
c = 98.165	γ = 120

Symmetry
Space Group	P 32 2 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 EIGER2 XE 16M		2024-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.06	98.17	98.5	0.99	13.5	10.2		51068

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.06	1.08			0.35

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1EW4	1.06	38.526	51068	1882	98.442	0.219	0.2178	0.2191	0.2476	0.2484	15.903

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]
-0.192	-0.096		-0.192		0.624

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.621
r_dihedral_angle_6_deg	15.611
r_dihedral_angle_3_deg	13.267
r_lrange_it	5.728
r_dihedral_angle_1_deg	5.363
r_scangle_it	4.272
r_scbond_it	2.838
r_angle_refined_deg	2.301
r_mcangle_it	1.467
r_mcbond_it	1.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.621
r_dihedral_angle_6_deg	15.611
r_dihedral_angle_3_deg	13.267
r_lrange_it	5.728
r_dihedral_angle_1_deg	5.363
r_scangle_it	4.272
r_scbond_it	2.838
r_angle_refined_deg	2.301
r_mcangle_it	1.467
r_mcbond_it	1.016
r_symmetry_nbd_refined	0.389
r_nbtor_refined	0.315
r_xyhbond_nbd_refined	0.255
r_nbd_refined	0.228
r_symmetry_xyhbond_nbd_refined	0.193
r_chiral_restr	0.176
r_gen_planes_refined	0.013
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	863
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.