1OJT | pdb_00001ojt

STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LVL	DLDH OF PSEUDOMONAS PUTIDA, PDB ENTRY 1LVL.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		BRIGHT YELLOW CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES USING HANGING DROP DIFFUSION METHOD AT ROOM TEMPERATURE. RESERVOIR: 1 ML CONTAINING 0.1M POTASSIUM PHOSPHATE AND 2M AMMONIUM SULFATE (PH 7.0). PRISM CRYSTALS TYPICALLY IN TWO WEEKS AT ROOM TEMPERATURE., vapor diffusion - hanging drop THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDES A FAD COFACTOR BUT NOT THE NADH. THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDE A FAD COFACTOR BUT NOT THE NADH.

Crystal Properties
Matthews coefficient	Solvent content
2.73	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.05	α = 90
b = 138.05	β = 90
c = 79.77	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	IMAGE PLATE	MAR scanner 300 mm plate	MULTILAYER MIRROR		M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LURE		LURE

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	2.7	40	94	0.066	18	7		11724		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	2.7	2.9	70		0.19	4	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT AND MIR	DLDH OF PSEUDOMONAS PUTIDA, PDB ENTRY 1LVL.	2.75	18	15850			0.173		0.232

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
p_transverse_tor	28
p_staggered_tor	24
p_planar_tor	2.3
p_multtor_nbd	0.33
p_xyhbond_nbd	0.24
p_singtor_nbd	0.23
p_chiral_restr	0.08
p_planar_d	0.055
p_angle_d	0.05
p_bond_d	0.02
p_plane_restr	0.01
p_angle_deg
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3556
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	53

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALEIT	data reduction
SHARP	phasing
PROLSQ	refinement
CCP4	data reduction
CCP4	data scaling