2IGM | pdb_00002igm

Crystal structure of recombinant pyranose 2-oxidase H548N mutant

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	298	12-13% monomethyl ether PEG 2000, 0.1 M mes, 50 mM CaCl2, 25% glycerol , pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.431	α = 90
b = 103.142	β = 106.08
c = 168.915	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 4		2004-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9393	ESRF	ID14-4

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	1.9	20	97	0.074	8.2	3.7	414274	436427

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	1.9	20	422203	417976	4236	96.74	0.15209	0.15209	0.15171	0.16	0.18913	0.2	RANDOM	14.984

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]
-0.17		-0.1	0.34		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.637
r_dihedral_angle_4_deg	14.042
r_dihedral_angle_3_deg	13.44
r_dihedral_angle_1_deg	6.819
r_scangle_it	3.625
r_scbond_it	2.598
r_angle_refined_deg	1.734
r_mcangle_it	1.552
r_mcbond_it	1.368
r_angle_other_deg	0.989
r_symmetry_vdw_other	0.32
r_symmetry_vdw_refined	0.276
r_mcbond_other	0.268
r_nbd_refined	0.233
r_nbd_other	0.216
r_xyhbond_nbd_refined	0.206
r_symmetry_hbond_refined	0.193
r_chiral_restr	0.182
r_nbtor_refined	0.176
r_xyhbond_nbd_other	0.164
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	36480
Nucleic Acid Atoms
Solvent Atoms	4255
Heterogen Atoms	520

Software

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