1XM8 | pdb_00001xm8

X-RAY STRUCTURE OF GLYOXALASE II FROM ARABIDOPSIS THALIANA GENE AT2G31350

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	293	10 MG/ML PROTEIN, 0.100 SODIUM ACETATE, 16 PERCENT PEG 4K, 10 PERCENT PEG 400, 0.200 GLYCINE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.494	α = 90
b = 58.782	β = 109.22
c = 69.049	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	BENT CYLINDRICAL SI- MIRROR (RH COATING)	2004-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D		APS	14-BM-D

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	1.742	33.72	97.4	0.079	21.2	7.6		51949

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)
	1.74	1.8	92.9		0.545	4.34	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	1.74	33.71	49295	2630	97.7	0.142	0.14	0.15	0.189	0.2	RANDOM	14.89

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]
0.442		0.012	0.206		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.794
r_dihedral_angle_4_deg	18.904
r_dihedral_angle_3_deg	14.118
r_scangle_it	6.477
r_dihedral_angle_1_deg	6.249
r_scbond_it	4.976
r_sphericity_bonded	2.927
r_mcangle_it	2.633
r_mcbond_it	2.284
r_sphericity_free	2.033
r_angle_refined_deg	1.746
r_angle_other_deg	0.884
r_mcbond_other	0.379
r_symmetry_vdw_refined	0.28
r_symmetry_hbond_refined	0.237
r_nbd_refined	0.229
r_symmetry_vdw_other	0.209
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.179
r_metal_ion_refined	0.116
r_chiral_restr	0.107
r_nbtor_other	0.087
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4027
Nucleic Acid Atoms
Solvent Atoms	562
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
ARP/wARP	model building
RESOLVE	phasing
REFMAC	refinement