Experiment: 3NDR

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EW8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Sodium acetate, 0.1M Tris-HCl, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.203	α = 90
b = 51.109	β = 89.36
c = 91.732	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 210		2010-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.979	SPring-8	BL38B1

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	2.88	50	97.4	0.108	9.9	2.1		16995			16.8

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	2.88	3	97.1		0.43	2.5	1.9	3280

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2EW8	2.88	39.733	1.34	16988	916	97.09	0.188	0.1848	0.1864	0.248	0.2461	RANDOM	27.5892

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]
4.8938		10.4744	-3.5057		-1.3882

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.913
f_angle_d	1.173
f_chiral_restr	0.075
f_bond_d	0.009
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7148
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	176

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement