3GFF | pdb_00003gff

Crystal structure of IroE-like serine hydrolase (NP_718593.1) from SHEWANELLA ONEIDENSIS at 2.12 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	15.0000% Ethanol, 0.2000M MgCl2, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.65	α = 90
b = 125.57	β = 117.94
c = 56.75	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-11-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162,0.97824,0.97864	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	2.12	28.307	79	0.058	8.62			33406		-3	25.019

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	2.12	2.2	77.9		0.276	2

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	2.12	28.307	33377	1684	88.55	0.187	0.184	0.19	0.241	0.24	RANDOM	25.264

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]
0.96		-0.14	-0.09		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.71
r_dihedral_angle_4_deg	13.952
r_dihedral_angle_3_deg	13.858
r_dihedral_angle_1_deg	3.62
r_angle_refined_deg	1.614
r_scangle_it	1.457
r_mcangle_it	1.416
r_scbond_it	1.007
r_angle_other_deg	0.99
r_mcbond_it	0.982
r_symmetry_vdw_other	0.358
r_mcbond_other	0.276
r_nbd_refined	0.215
r_nbd_other	0.2
r_symmetry_vdw_refined	0.189
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.183
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.101
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4985
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction