3DYI | pdb_00003dyi

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

X-RAY DIFFRACTION

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
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.442	α = 90
b = 47.442	β = 90
c = 174.18	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	2006-12-08	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	1.6	33.54	94.4	0.048	14.5	4.4	31093	29366

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3DKR	1.72	33.54	25016	24097	1241	95.84	0.178	0.178	0.177	0.19	0.201	0.21	RANDOM	25.404

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]
0.33	0.16		0.33		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.822
r_dihedral_angle_4_deg	15.923
r_dihedral_angle_3_deg	11.56
r_dihedral_angle_1_deg	5.199
r_scangle_it	1.741
r_scbond_it	1.131
r_angle_refined_deg	1.03
r_mcangle_it	0.688
r_mcbond_it	0.405
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.822
r_dihedral_angle_4_deg	15.923
r_dihedral_angle_3_deg	11.56
r_dihedral_angle_1_deg	5.199
r_scangle_it	1.741
r_scbond_it	1.131
r_angle_refined_deg	1.03
r_mcangle_it	0.688
r_mcbond_it	0.405
r_nbtor_refined	0.304
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.167
r_symmetry_hbond_refined	0.091
r_xyhbond_nbd_refined	0.085
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1837
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	1

Software

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

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.