2QEZ | pdb_00002qez

Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 30.0% 2-methyl-2,4-pentanediol, 0.2M Magnesium acetate, 0.1M Sodium pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.33	α = 90
b = 223.7	β = 90
c = 65.93	γ = 90

Symmetry
Space Group	P 21 21 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 325 mm CCD	Flat mirror (vertical focusing)	2007-02-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162, 0.97925, 0.97895	SSRL	BL11-1

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	2.15	29.21	98.9	0.054	9.26			162506		-3	44.807

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	2.15	2.17	94.6		0.487	1.5

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	MAD	THROUGHOUT	2.15	29.21	161942	8067	99.27	0.23	0.228	0.24	0.279	0.29	RANDOM	48.229

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]
-2.31			-1.03		3.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.243
r_dihedral_angle_4_deg	15.271
r_dihedral_angle_3_deg	11.528
r_scangle_it	6.576
r_scbond_it	4.918
r_dihedral_angle_1_deg	3.402
r_mcangle_it	2.663
r_mcbond_it	1.662
r_angle_refined_deg	1.594
r_angle_other_deg	1.085
r_mcbond_other	0.685
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.197
r_symmetry_vdw_other	0.189
r_nbtor_refined	0.178
r_symmetry_hbond_refined	0.169
r_nbd_other	0.161
r_symmetry_vdw_refined	0.113
r_nbtor_other	0.09
r_xyhbond_nbd_other	0.073
r_chiral_restr	0.063
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19677
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing