2YAJ | pdb_00002yaj

CRYSTAL STRUCTURE OF GLYCYL RADICAL ENZYME with bound substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R9D	PDB ENTRY 1R9D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			22 % PEG MME 550, 30 MM MGCL2, 100 MM TRIS/HCL PH 7.5 - 8.4 .

Crystal Properties
Matthews coefficient	Solvent content
2.56	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.049	α = 90
b = 228.588	β = 90
c = 148.226	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	MARRESEARCH	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591

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	1.81	29.16	99	0.09	13	5		202600		2	19.24

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	1.81	1.88	99		0.33	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1R9D	1.813	29.157	1.36	202600	10130	99.82	0.1909	0.1881	0.1802	0.2442	0.2365

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]
-0.8218			0.1873		0.6344

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.228
f_angle_d	1.612
f_chiral_restr	0.094
f_bond_d	0.017
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14976
Nucleic Acid Atoms
Solvent Atoms	2098
Heterogen Atoms	54

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
AMoRE	phasing
SHARP	phasing
PHENIX	refinement