1YKK | pdb_00001ykk

Protocatechuate 3,4-Dioxygenase Y408C Mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Ohlendorf et al (1988) Nature, 336, 403-405.

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 194.87	α = 90
b = 126.961	β = 96.39
c = 132.764	γ = 90

Symmetry
Space Group	I 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						M	SINGLE WAVELENGTH

Data Collection

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3,4 PCD	2.06	26.09	142392	183721	1608	93.1	0.21	0.21	0.2038	0.219	0.2072	RANDOM	36.2

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]
-5.41		1.59	-0.76		6.17

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.5
c_angle_deg	1.6
c_improper_angle_d	1.48
c_bond_d	0.012
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
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20664
Nucleic Acid Atoms
Solvent Atoms	792
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CNS	refinement