4GQA | pdb_00004gqa

Crystal structure of NAD binding oxidoreductase from Klebsiella pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	20% (w/v) PEG 3350, 0.2M di-Amonium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.418	α = 90
b = 113.026	β = 90.54
c = 132.174	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 225 mm CCD	beryllium lens	2012-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.42	50	99.4	0.091	21.7	4.3	65155	65155		-3

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	2.42	2.46	98.9		0.648	2.2	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.42	50	61607	61607	3272	99.3	0.18805	0.18584	0.18	0.22978	0.22	RANDOM	52.332

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]
-2.36		-0.34	6.45		-4.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.495
r_dihedral_angle_4_deg	20.007
r_dihedral_angle_3_deg	15.97
r_dihedral_angle_1_deg	6.01
r_angle_refined_deg	1.641
r_angle_other_deg	1.385
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11513
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	41

Software

Software
Software Name	Purpose
HKL-3000	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing