1YQC | pdb_00001yqc

Crystal Structure of Ureidoglycolate Hydrolase (AllA) from Escherichia coli O157:H7

X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.18	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.047	α = 90
b = 74.466	β = 103.894
c = 56.364	γ = 90

Symmetry
Space Group	P 1 21 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 4	Mirrors	2004-10-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.9611, 0.9800, 0.9802	NSLS	X8C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.71	50	96.2				36248

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	1.71	1.77		99.5	0.375

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MAD	THROUGHOUT	1.709	36.442	1.71	70830	35732	1782	95.458	0.228	0.228	0.2262	0.225	0.269	0.2678	RANDOM	22.234

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]
-0.064		-0.018	0.116		-0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.353
r_dihedral_angle_4_deg	18.348
r_dihedral_angle_3_deg	17.345
r_dihedral_angle_1_deg	6.84
r_scangle_it	4.091
r_scbond_it	2.768
r_mcangle_it	1.888
r_angle_refined_deg	1.76
r_mcbond_it	1.276
r_symmetry_vdw_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.353
r_dihedral_angle_4_deg	18.348
r_dihedral_angle_3_deg	17.345
r_dihedral_angle_1_deg	6.84
r_scangle_it	4.091
r_scbond_it	2.768
r_mcangle_it	1.888
r_angle_refined_deg	1.76
r_mcbond_it	1.276
r_symmetry_vdw_refined	0.313
r_nbtor_refined	0.306
r_nbd_refined	0.233
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.135
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2554
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction

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.