2HBV

Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.75	298	15% PEG 5000, 0.2M MgCl2, pH 8.75, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.557	α = 90
b = 48.107	β = 127.31
c = 110.7	γ = 90

Symmetry
Space Group	C 1 2 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 315		2005-02-17	M	MAD
2	1
3	1
4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97904, 0.97918, 0.97818, 0.98034, 0.97951	APS	19-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	1.65	50	46.8	0.028	13.9	1.6		72711	2	2

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	1.65	1.71	22.1		0.189		1.2	1713

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.65	33.81	69090	3532	95.17	0.251	0.211	0.251	RANDOM	41.7

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]
-0.16		-0.07	0.24		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.087
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	14.815
r_dihedral_angle_1_deg	5.587
r_scangle_it	2.115
r_scbond_it	1.426
r_angle_refined_deg	1.224
r_mcangle_it	1.037
r_mcbond_it	0.638
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.087
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	14.815
r_dihedral_angle_1_deg	5.587
r_scangle_it	2.115
r_scbond_it	1.426
r_angle_refined_deg	1.224
r_mcangle_it	1.037
r_mcbond_it	0.638
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.268
r_symmetry_hbond_refined	0.213
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.115
r_metal_ion_refined	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5165
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.