4FGC | pdb_00004fgc

Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F8B	PDB ENTRY 4F8B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.4	293.15	16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride, VAPOR DIFFUSION, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.048	α = 90
b = 93.048	β = 90
c = 193.651	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	200	CCD	ADSC QUANTUM 315r	mirrors	2011-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	1.000003	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.498	22.151	91.6	0.14	6.8	4	34498	31577			46.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.498	2.54	88.8		0.65	2.3	3.9	1498

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 (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	PDB ENTRY 4F8B	2.498	22.15	34397	29866	1592	91.46	0.23225	0.22836	0.23	0.30485	0.3	RANDOM	39.309

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]
0.36	0.18		0.36		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.833
r_dihedral_angle_4_deg	11.448
r_dihedral_angle_3_deg	11.073
r_scangle_it	3.033
r_dihedral_angle_1_deg	2.322
r_angle_refined_deg	1.997
r_scbond_it	1.856
r_mcangle_it	1.424
r_mcbond_it	0.744
r_chiral_restr	0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.833
r_dihedral_angle_4_deg	11.448
r_dihedral_angle_3_deg	11.073
r_scangle_it	3.033
r_dihedral_angle_1_deg	2.322
r_angle_refined_deg	1.997
r_scbond_it	1.856
r_mcangle_it	1.424
r_mcbond_it	0.744
r_chiral_restr	0.046
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6007
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	84

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

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.