Experiment: 9FZF

Transcriptional repressor NrdR from E. coli, ADP/dATP bound state

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7P3F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1 M Bis-Tris pH 5.5, 0.2 M ammonium acetate, 45% (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.126	α = 90
b = 147.126	β = 90
c = 85.805	γ = 120

Symmetry
Space Group	P 62 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 EIGER2 X 16M		2020-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.444	127.42	95.1	0.31	0.315	0.05	0.999	10.6	39.1		10132

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	2.444	2.699	84.7		2.635	2.667	0.413	0.912	1.6	41.2

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.444	127.42	10312	494	49.6	0.2181	0.2149	0.2831	0.2059	RANDOM	47.34

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]
3.3756			3.3756		-6.7511

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.14
t_omega_torsion	2.76
t_angle_deg	0.85
t_bond_d	0.007
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	2404
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	118

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing