5Z1X

Crystal Structure of Laccase from Cerrena sp. RSD1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293	1.4M ammonium sulfate, pH 7.6

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.626	α = 90
b = 88.795	β = 90
c = 147.815	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	RAYONIX MX300HE		2013-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

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	1.38	30	98.6	0.042	44.2	4.3		228137

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	1.38	1.43	95		0.27	4.8	2.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GYC	1.38	25	216276	11402	98.64	0.12719	0.12602	0.14948	RANDOM	17.117

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]
			0.41		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.106
r_sphericity_free	25.905
r_dihedral_angle_4_deg	18.919
r_dihedral_angle_3_deg	10.167
r_sphericity_bonded	6.534
r_dihedral_angle_1_deg	6.396
r_long_range_B_refined	2.96
r_long_range_B_other	2.96
r_angle_refined_deg	1.156
r_rigid_bond_restr	1.055
r_scangle_other	0.976
r_mcangle_it	0.909
r_mcangle_other	0.909
r_scbond_it	0.856
r_scbond_other	0.856
r_angle_other_deg	0.709
r_mcbond_it	0.708
r_mcbond_other	0.708
r_chiral_restr	0.067
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7488
Nucleic Acid Atoms
Solvent Atoms	1596
Heterogen Atoms	150

Software

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