2UZ1

1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-methyl- 2,4-pentanediol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AG0	PDB ENTRY 2AG0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.1 M TRIS/HCL, PH 7.5, 0.2 M POTASSIUM ISOTHIOCYANATE, 10% (W/V) POLYETHYLENE GLYCOL 1000 MW, 10% POLYETHYLENE GLYCOL 8000 MW, AND 2-METHYLPENTANE-2-4-DIOL 45% (V/V); PROTEIN CONCENTRATION 5 MG ML-1 WITH A THREEFOLD STOICHIOMETRIC EXCESS OF THIAMINE DIPHOSPHATE (THDP).

Crystal Properties
Matthews coefficient	Solvent content
1	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.462	α = 90
b = 121.601	β = 90
c = 162.957	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	ADSC CCD		2005-11-05	M	SINGLE WAVELENGTH

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

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	1.65	50	99	0.13	5.5	5.1		249612

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	1.65	1.68	100		0.88	1.5	5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2AG0	1.65	97.59	236875	12534	99.7	0.168	0.167	0.192	RANDOM	12.59

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]
-0.32			0.75		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.238
r_dihedral_angle_4_deg	18.7
r_dihedral_angle_3_deg	12.38
r_dihedral_angle_1_deg	5.608
r_scangle_it	2.877
r_scbond_it	1.835
r_angle_refined_deg	1.27
r_mcangle_it	0.967
r_mcbond_it	0.561
r_nbtor_refined	0.303
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.191
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	16184
Nucleic Acid Atoms
Solvent Atoms	1881
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing