3DLT | pdb_00003dlt

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	1R1D

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	40.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.848	α = 90
b = 46.848	β = 90
c = 173.954	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	2006-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	40.57	96.6	0.091	6.5	5.85	30410	29364

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	1R1D	1.9	40.57	18460	18336	928	99.94	0.208	0.208	0.205	0.22	0.255	0.25	RANDOM	42.49

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]
2.67	1.33		2.67		-4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.582
r_dihedral_angle_3_deg	13.591
r_dihedral_angle_4_deg	12.667
r_dihedral_angle_1_deg	6.353
r_scangle_it	2.521
r_scbond_it	1.762
r_angle_refined_deg	1.361
r_mcangle_it	1.168
r_angle_other_deg	0.887
r_mcbond_it	0.743
r_symmetry_vdw_other	0.297
r_nbd_refined	0.21
r_nbtor_refined	0.186
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.153
r_mcbond_other	0.151
r_symmetry_hbond_refined	0.121
r_nbtor_other	0.088
r_chiral_restr	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1834
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	12

Software

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