2D81 | pdb_00002d81

PHB depolymerase (S39A) complexed with R3HB trimer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D80	PDB entry 2D80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	294	2.0M sodium chloride, 0.1M acetate-NaOH, 5% 1,4-dioxane, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.934	α = 90
b = 48.863	β = 94.45
c = 64.198	γ = 90

Symmetry
Space Group	C 1 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	90	CCD	ADSC QUANTUM 4	mirrors	2005-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.0000	SPring-8	BL44B2

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	1.66	40.84	98.3	0.084	25.9			29362			11.3

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	1.66	1.72	89.9		0.262	0.262

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2D80	1.66	40.84	29362	2930	97.9	0.176	0.176	0.203	RANDOM	10.4

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]
-1.66		3.68	-1.61		3.27

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25
c_scangle_it	2.33
c_scbond_it	1.69
c_mcangle_it	1.42
c_mcbond_it	1.01
c_angle_deg	0.9
c_improper_angle_d	0.71
c_bond_d	0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2356
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	33

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing