3E1G

Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	6	298	PEG 8000, Na acetate, pH 6.0, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.322	α = 90
b = 47.322	β = 90
c = 174.741	γ = 120

Symmetry
Space Group	P 32 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	120	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Blue	2006-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	1.49	33.52	90.6	0.157	5.1	7.6	38533	34921

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1R1D	2.2	33.52	11933	11667	578	99.98	0.2	0.2	0.198	0.249	RANDOM	42.325

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]
1.51	0.75		1.51		-2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.882
r_dihedral_angle_3_deg	15.014
r_dihedral_angle_4_deg	13.851
r_dihedral_angle_1_deg	8.167
r_angle_refined_deg	0.802
r_angle_other_deg	0.682
r_symmetry_vdw_other	0.318
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.225
r_nbd_other	0.212
r_nbtor_refined	0.195
r_xyhbond_nbd_refined	0.159
r_symmetry_hbond_refined	0.149
r_nbtor_other	0.104
r_chiral_restr	0.098
r_xyhbond_nbd_other	0.071
r_bond_refined_d	0.023
r_gen_planes_refined	0.021
r_bond_other_d	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1793
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	8

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
Crystal	data reduction