6OR9 | pdb_00006or9

Structure of L-lactate dehydrogenase from Trichoplusia ni

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	MCSG1 H11: 25% (W/V) PEG 3350, 200MM SODIUM CHLORIDE, 100MM HEPES FREE ACID / NAOH PH 7.5: TRNIA.00711.a.GL11.PS38300 AT 14.3 MG/ML + 2MM ATP: CRYO: 15% EG + BSI1767: TRAY 295240 H11: PUCK DAC0-8 FOR EXPERIMENTAL PHASING, A CRYSTAL FROM THE SAME DROP WAS INCUBATED FOR 15 SEC IN A SOLUTION OF 85% RESERVOIR AND 15% 2.5M SODIUM IODIDE IN ETHYLENE GLYCOL (FINAL IODIDE CONCENTRATION 375MM), AND VITRIFIED IN LIQUID NITROGEN: TRAY 295240H11: PUCK ANX5-15. THE PROTEIN WAS ACCIDENTALLY PURIFIED FROM A CULTURE THAT WAS SUPPOSED TO EXPRESS SSGCID PROTEIN PLFAA.18754.A.GL11., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.39	α = 113.06
b = 76.48	β = 109.84
c = 79.52	γ = 88.7

Symmetry
Space Group	P 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	RAYONIX MX-300		2018-11-29	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2018-11-30	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
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.8	48.906	96.7	0.039	17.55	2.951		115247			30.18

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	1.8	1.85	93.1		0.344	2.74	2.68

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.8	48.91	1.98	115226	1971	97	0.159	0.158	0.1601	0.195	0.1981	0	29.42

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
f_dihedral_angle_d	12.316
f_angle_d	0.87
f_chiral_restr	0.06
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9055
Nucleic Acid Atoms
Solvent Atoms	1097
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
PARROT	phasing