3DKR | pdb_00003dkr

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	PDB ENTRY 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
2.11	41.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.225	α = 90
b = 47.225	β = 90
c = 174.572	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	CONFOCAL	2006-12-05	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	30	99.8	0.048	25.4	10.9	30909	30848

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	PDB ENTRY 1R1D	1.6	29.84	30917	30844	1549	99.8	0.167	0.167	0.167	0.17	0.184	0.19	RANDOM	20.895

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]
0.49	0.25		0.49		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.857
r_dihedral_angle_3_deg	11.651
r_dihedral_angle_4_deg	10.755
r_dihedral_angle_1_deg	5.865
r_scangle_it	2.335
r_scbond_it	1.636
r_angle_refined_deg	1.234
r_mcangle_it	1.004
r_angle_other_deg	0.89
r_mcbond_it	0.622
r_symmetry_vdw_other	0.297
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.22
r_nbtor_refined	0.183
r_nbd_other	0.179
r_mcbond_other	0.158
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.107
r_nbtor_other	0.084
r_chiral_restr	0.077
r_bond_refined_d	0.009
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	1843
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	8

Software

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