Experiment: 2XXJ

Penta mutant of lactate dehydrogenase from Thermus thermophilus, ternary complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V7P	PDB ENTRY 2V7P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1M NACACODYLATE 0.2M NAAC PH 6.5, 15% W/V PEG 8000. DROPLETS = 2.0 MICROL PROTEIN, 2 MICROL PRECIPITANT, 0.5 MICROL ADDITIVE (30% D(PLUS)-GLUCOSE MONOHYDRATE).

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.15	α = 90
b = 147.36	β = 90
c = 152.28	γ = 90

Symmetry
Space Group	P 21 21 21

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 CCD	MIRRORS	2010-01-31	M	SINGLE WAVELENGTH

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

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	1.96	105.9	98.9	0.07	20.94	7.37		91523		-3	25.04

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	1.96	2.08	93.4		0.44	3.32	4.91

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2V7P	1.964	67.644	1.34	91516	4577	98.89	0.1777	0.1752	0.1735	0.2263	0.223	29.13

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]
4.0938			-4.0562		-0.0376

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.317
f_angle_d	1.137
f_chiral_restr	0.107
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9175
Nucleic Acid Atoms
Solvent Atoms	643
Heterogen Atoms	110

Software

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