3DIV | pdb_00003div

Crystal structure of laccase from Cerrena maxima at 1.76A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H5U	PDB ENTRY 2H5U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	50mM sodium citrate, 15%(w/v) PEG 6000, 0.04M Tris, malein, NaOH , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.581	α = 90
b = 77.101	β = 90
c = 130.884	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	MAR CCD 165 mm		2005-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8068	EMBL/DESY, HAMBURG	X13

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	1.76	19.07	96	0.18		4.87	52442	52442

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	1.76	1.8	91.8

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2H5U	1.76	7.99	54487	52442	2643	99.92	0.18251	0.18067	0.176	0.1812	0.21705	0.2156	RANDOM	15.972

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]
			0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.157
r_dihedral_angle_4_deg	17.844
r_dihedral_angle_3_deg	12.433
r_dihedral_angle_1_deg	6.436
r_scangle_it	2.191
r_scbond_it	1.531
r_angle_refined_deg	1.399
r_mcangle_it	0.982
r_mcbond_it	0.575
r_nbtor_refined	0.315
r_nbd_refined	0.257
r_symmetry_vdw_refined	0.165
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.116
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3792
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	157

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
XDS	data reduction
XDS	data scaling
PHASER	phasing