3GRO | pdb_00003gro

Human palmitoyl-protein thioesterase 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EI9	PDB entry 1EI9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.4	291	24% PEG 3350, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate. Cryoprotectant: 9 parts reservoir + 1 part 80% glycerol, pH 5.4, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.71	α = 90
b = 90.642	β = 90
c = 129.165	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	CCD	ADSC QUANTUM 315		2009-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-ID

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	2.53	50	100	0.17	6.1	8.8		21818

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)
	2.53	2.62	100		0.993		8.2	2130

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 1EI9	2.53	30	21649	1233	99.6	0.202	0.2	0.2165	0.238	0.2532	Thin shells	29.206

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]
1.1			-1.061		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.039
r_dihedral_angle_4_deg	17.237
r_dihedral_angle_3_deg	14.941
r_dihedral_angle_1_deg	5.644
r_mcangle_it	1.801
r_scangle_it	1.613
r_angle_refined_deg	1.081
r_scbond_it	1.045
r_mcbond_it	1.022
r_angle_other_deg	0.861
r_mcbond_other	0.131
r_chiral_restr	0.064
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4235
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction
HKL-2000	data scaling