2WXD | pdb_00002wxd

A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E4M	PDB ENTRY 1E4M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		TRIS-HCL PH 8, 68 % SAT AMMONIUM SULFATE; PROTEIN IN HEPES PH 6.5, 150 MM NACL, 0.02 MM ZNSO4; HANGING DROPS 2 AND 2 UL

Crystal Properties
Matthews coefficient	Solvent content
2.56	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.245	α = 90
b = 137.567	β = 90
c = 80.723	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC CCD		2008-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.6	80.85	99.7	0.08	5.9	4.63		99631			15.4

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	1.6	1.69	98.4		0.38	1.71	3.87

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 (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 1E4M	1.6	68.78	94531	5075	99.84	0.14368	0.14257	0.15	0.16408	0.17	RANDOM	12.436

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.636
r_dihedral_angle_4_deg	13.544
r_dihedral_angle_3_deg	11.154
r_scangle_it	6.503
r_dihedral_angle_1_deg	6.264
r_scbond_it	5.507
r_angle_refined_deg	2.574
r_mcangle_it	2.533
r_angle_other_deg	1.662
r_mcbond_it	1.516
r_mcbond_other	0.539
r_nbd_refined	0.374
r_symmetry_hbond_refined	0.32
r_symmetry_vdw_other	0.289
r_symmetry_vdw_refined	0.242
r_xyhbond_nbd_refined	0.205
r_nbd_other	0.202
r_nbtor_refined	0.198
r_chiral_restr	0.174
r_metal_ion_other	0.1
r_nbtor_other	0.097
r_xyhbond_nbd_other	0.06
r_bond_refined_d	0.03
r_gen_planes_refined	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4007
Nucleic Acid Atoms
Solvent Atoms	764
Heterogen Atoms	386

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling