3G9Z | pdb_00003g9z

Crystal structure of EstE5, was soaked by p-nitrophenyl caprylate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295.5	0.1M Tris-HCl pH 7.0-7.5, 1.8-2.2M ammonium sulfate, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.896	α = 90
b = 60.896	β = 90
c = 145.368	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2008-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.000	PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	50	98.1				14373	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	95.8

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3FAK	2.2	37.92	14373	13639	717	98.33	0.19249	0.19249	0.18865	0.27192	0.2629	RANDOM	41.6

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			-0.49		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.305
r_dihedral_angle_4_deg	21.415
r_dihedral_angle_3_deg	20.713
r_dihedral_angle_1_deg	7.202
r_scangle_it	4.438
r_scbond_it	3.185
r_angle_refined_deg	2.19
r_mcangle_it	1.822
r_mcbond_it	1.261
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.283
r_nbd_refined	0.24
r_chiral_restr	0.162
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.057
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2241
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling