3KRZ

Crystal Structure of the Thermostable NADH4-bound old yellow enzyme from Thermoanaerobacter pseudethanolicus E39

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	298	50mM Magnesium formate, pH 7.0, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.38	α = 90
b = 98.556	β = 92.4
c = 95.134	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 315r		2008-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.501	97.59	91.8	0.065	0.065	10.6	2.7		229398

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.58	57.9		0.395	0.395	1.9	1.3	20931

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	31.69	139844	7379	98.82	0.157	0.15654	0.19397	RANDOM	15.302

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	38.042
r_dihedral_angle_4_deg	13.527
r_dihedral_angle_3_deg	12.46
r_dihedral_angle_1_deg	5.467
r_scangle_it	3.524
r_scbond_it	2.19
r_angle_refined_deg	1.313
r_mcangle_it	1.263
r_mcbond_it	0.902
r_nbtor_refined	0.306
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.16
r_symmetry_vdw_refined	0.141
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10511
Nucleic Acid Atoms
Solvent Atoms	1690
Heterogen Atoms	277

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction