3DYV

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DKR

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
2.05	39.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.154	α = 90
b = 47.154	β = 90
c = 174.226	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	2006-12-18	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	1.81	33.4	88.1	0.054	12	5.24	41855	36866

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	3DKR	1.81	33.4	21248	20296	1078	99.87	0.197	0.197	0.195	0.227	RANDOM	29.854

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]
1.05	0.52		1.05		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.83
r_dihedral_angle_4_deg	17.217
r_dihedral_angle_3_deg	10.671
r_dihedral_angle_1_deg	5.248
r_scangle_it	1.311
r_angle_refined_deg	0.996
r_scbond_it	0.934
r_angle_other_deg	0.861
r_mcangle_it	0.632
r_mcbond_it	0.395
r_symmetry_vdw_other	0.291
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.203
r_nbtor_refined	0.176
r_nbd_other	0.173
r_symmetry_hbond_refined	0.104
r_xyhbond_nbd_refined	0.103
r_nbtor_other	0.083
r_mcbond_other	0.067
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1823
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	1

Software

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