2YB4 | pdb_00002yb4

Structure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202) with bound SO4, no metal

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.1		PROTEIN (15 MG/ML IN 10 MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL) ADDED TO 25% PEG 3350, 100 MM BIS-TRIS PH 6.1, 200 MM AMSO4. CRYOSOLUTION WAS RESERVOIR WITH 20% ETHYLENE GLYCOL

Crystal Properties
Matthews coefficient	Solvent content
1.95	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.07	α = 90
b = 46.53	β = 90
c = 130.49	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.2	46	99.7	0.1	10.3	3.8		12953			12.86

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	2.2	2.32	100		0.26	4.8	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	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	SIRAS	NONE	2.2	31.775	12440	610	95.74	0.1735	0.1704	0.17	0.2327	0.23

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]
9.5437			0.8447		4.8597

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.318
f_angle_d	1.053
f_chiral_restr	0.087
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2136
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	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.