4F8B | pdb_00004f8b

Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF

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, HANGING DROP	7.4	293.15	16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride or magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.507	α = 90
b = 93.507	β = 90
c = 193.696	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	2006-04-10	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	2.502	41.56	98.7	0.102	7.8	9.9	34623	34623	1	1	54.7

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	2.502	2.57	89.9		0.29	2.1	6.5

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3BP1	2.502	41.56	33897	32475	1720	98.72	0.19334	0.18918	0.2	0.27195	0.27	RANDOM	42.536

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]
1.93	0.96		1.93		-2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.639
r_dihedral_angle_3_deg	19.63
r_dihedral_angle_4_deg	19.121
r_dihedral_angle_1_deg	7.533
r_scangle_it	4.348
r_scbond_it	2.923
r_mcangle_it	2.21
r_angle_refined_deg	2.057
r_mcbond_it	1.339
r_nbtor_refined	0.329

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.639
r_dihedral_angle_3_deg	19.63
r_dihedral_angle_4_deg	19.121
r_dihedral_angle_1_deg	7.533
r_scangle_it	4.348
r_scbond_it	2.923
r_mcangle_it	2.21
r_angle_refined_deg	2.057
r_mcbond_it	1.339
r_nbtor_refined	0.329
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.251
r_metal_ion_refined	0.238
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.129
r_bond_refined_d	0.024
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6013
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	85

Software

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