3RZP | pdb_00003rzp

Crystal Structure of the C194A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BP1	PDB ENTRY 3BP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.2 M Sodium acetate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.316	α = 110.43
b = 71.192	β = 119.22
c = 71.463	γ = 99.33

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315r	mirrors	2010-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97937	APS	19-ID

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	2	50	95.8	0.078	8.7	1.8	68972	68972			32.69

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	2	2.03	93.2		0.37	1.9	1.6	3394

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 3BP1	2	35.024	67907	67907	3446	95.66	0.174	0.174	0.171	0.17	0.221	0.22	random	43

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]
-4.4282	-6.8809	3.7935	-5.7593	0.3931	10.1875

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.726
f_angle_d	1.217
f_chiral_restr	0.098
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8230
Nucleic Acid Atoms
Solvent Atoms	470
Heterogen Atoms	64

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.