3K4K | pdb_00003k4k

Pyranose 2-oxidase F454N mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	298	0.1M MES, 50MM MGCL2, 10% (W/V)% MONOMETHYLETHER PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.059	α = 90
b = 102.059	β = 90
c = 119.693	γ = 90

Symmetry
Space Group	P 42 21 2

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	MARRESEARCH	MIRRORS	2008-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.0379	MAX II	I911-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.6	30	99.9	0.1	18.1	12.9	83548	83548

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7	99.6		0.86	3.1	9.9	13637

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 2IGO	1.6	30	81587	81587	1961	99.88	0.18556	0.18556	0.18488	0.19	0.2129	0.22	RANDOM	12.416

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]
-0.49			-0.49		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.291
r_dihedral_angle_4_deg	16.281
r_dihedral_angle_3_deg	12.474
r_dihedral_angle_1_deg	6.871
r_scangle_it	3.699
r_scbond_it	2.739
r_angle_refined_deg	1.841
r_mcangle_it	1.663
r_mcbond_it	1.426
r_angle_other_deg	1.011
r_mcbond_other	0.363
r_symmetry_vdw_other	0.261
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.235
r_xyhbond_nbd_other	0.223
r_nbd_other	0.213
r_nbtor_refined	0.185
r_chiral_restr	0.161
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.119
r_nbtor_other	0.092
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4531
Nucleic Acid Atoms
Solvent Atoms	436
Heterogen Atoms	53

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling