Experiment: 30OH

Pyrococcus abyssi Rubredoxin @ 0.43 Angstrom resolution, Transferable Aspherical Atom Model (TAAM) refinement

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9TA4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	291	3.6 - 3.8 M Sodium Malonate (pH 6.0)

Crystal Properties
Matthews coefficient	Solvent content
1.8	29.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.73	α = 90
b = 39.237	β = 90
c = 45.14	γ = 90

Symmetry
Space Group	P 21 21 21

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 X CdTe 16M	19 Beryllium compound refractive lenses, proximal slits (20 cm from sample)	2025-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.38573	PETRA III, EMBL c/o DESY	P14 (MX2)

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	0.433	20.921	96.2	0.0562	0.0573	0.011	1	23.92	26.62		245905

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)
	0.433	0.464	59.9		1.8678	1.923	0.4541	0.621	1.66	17.76	12295

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	0.434	20.92	245522	12376	85.1	0.0653	0.0651	0.0754	0.0693	0.079	RANDOM	4.65

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]
-0.2461			-0.0451		0.2912

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.02
t_omega_torsion	6.74
t_angle_deg	2.59
t_bond_d	0.033
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	433
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	4

Software

Software
Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
autoPROC	data processing
Aimless	data scaling
STARANISO	data scaling
BUSTER	phasing
BUSTER	refinement

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.