2Q35 | pdb_00002q35

Crystal Structure of the Y82F variant of ECH2 decarboxylase domain of CurF from Lyngbya majuscula

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q34	PDB ENTRY 2Q34

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.15	277.15	1.5M sodium malonate pH 7.0, 50 mM HEPES pH 6.8, 20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol, pH 7.15, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.138	α = 90
b = 106.138	β = 90
c = 119.497	γ = 120

Symmetry
Space Group	H 3 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	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2006-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

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	99.9	0.061	12.6	10.9	31133	31133	1	1	23.6

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	1.65	1.71	100		0.609	3.7	9.6	3069

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Q34	1.65	33.36	31133	31124	1571	99.7	0.169	0.167	0.19	0.204	0.21	RANDOM	21.465

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]
-1.64	-0.82		-1.64		2.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.188
r_dihedral_angle_4_deg	19.237
r_dihedral_angle_3_deg	14.076
r_scangle_it	5.966
r_dihedral_angle_1_deg	4.941
r_scbond_it	3.878
r_mcangle_it	1.761
r_angle_refined_deg	1.316
r_mcbond_it	1.206
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.188
r_dihedral_angle_4_deg	19.237
r_dihedral_angle_3_deg	14.076
r_scangle_it	5.966
r_dihedral_angle_1_deg	4.941
r_scbond_it	3.878
r_mcangle_it	1.761
r_angle_refined_deg	1.316
r_mcbond_it	1.206
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.268
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1894
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
PHASER	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.