3B59 | pdb_00003b59

Crystal structure of the Mn(II)-bound glyoxalase from Novosphingobium aromaticivorans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.2M MgCl2, 0.1M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.997	α = 90
b = 168.348	β = 90
c = 202.79	γ = 90

Symmetry
Space Group	I 2 2 2

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	MAR CCD 165 mm	SGX-CAT	2007-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.98000	APS	31-ID

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	2.53	31.69	99.9	0.137	19.9	15.1	160103	160103			29.6

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	2.53	2.67	100		0.54	4.8	15.2	24096

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.53	29.57	154584	7716	96.6	0.218	0.218	0.22	0.257	0.26	RANDOM	33.5

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]
-6.81			8.01		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.7
c_scangle_it	2.8
c_mcangle_it	1.9
c_scbond_it	1.89
c_angle_deg	1.5
c_mcbond_it	1.12
c_improper_angle_d	0.98
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13998
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CNS	refinement
CBASS	data collection
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
SHELXD	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.