5AOC | pdb_00005aoc

The structure of a novel thermophilic esterase from the Planctomycetes species, Thermogutta terrifontis, Est2-valerate bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EVQ	PDB ENTRY 1EVQ

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.64	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.991	α = 90
b = 70.874	β = 90
c = 75.932	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PIXEL			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	1.79	51.8	100	0.09	9.8	6.1		32257		1.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.9	100		1.1	1.6	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1EVQ	1.79	51.81	30305	1596	99.06	0.1875	0.18467	0.1943	0.24096	0.2447	RANDOM	30.184

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]
0.65			-1.51		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.804
r_dihedral_angle_4_deg	20.033
r_dihedral_angle_3_deg	15.646
r_scbond_it	6.161
r_dihedral_angle_1_deg	5.814
r_mcangle_it	5.238
r_mcbond_it	4.204
r_mcbond_other	4.194
r_angle_refined_deg	1.46
r_angle_other_deg	0.977
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2151
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
MOLREP	phasing