Experiment: 2YB1

Structure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202) with bound Mn, AMP and phosphate.

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) WITH 5MM MNCL2, 20 MM AMP ADDED TO 17% PEG 2000 MME, 100 MM BIS-TRIS PH 6.1. CRYO ML, 20% ETHYLENE GLYCOL, 1 MM MN, 2 MM AMP.

Crystal Properties
Matthews coefficient	Solvent content
1.95	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.958	α = 90
b = 46.765	β = 90
c = 130.785	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	1.9	40	96.9	0.08	12.9	5.3		19389			11.07

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	1.9	2	82.6		0.3	4.1	3.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	NONE	1.898	38.039	18950	968	94.12	0.1604	0.158	0.1571	0.2066

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]
0.0632			2.3032		1.6929

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.015
f_angle_d	1.127
f_chiral_restr	0.088
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2136
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	31

Software

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