3ZZN | pdb_00003zzn

5-Mutant (R79W, R151A, E279A, E299A,E313A) Lactate-Dehydrogenase from Thermus thermophillus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V6M	PDB ENTRY 2V6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	5-MUT TT-LDH WAS CRYSTALLIZED AT 10MG/ML BY THE HANGING-DROP VAPOUR-DIFFUSION METHOD, FOLLOWING THE MIXING OF THE PROTEIN AND THE MOTHER-LIQUOR SOLUTIONS AT A 1:1 RATIO. THE MOTHER LIQUOR SOLUTION WAS 0.1 M HEPES BUFFER PH 9, 18-20% PEG 6000, 2 M LICL2, 500 MICROMOLAR ADP. CRYSTALS GREW WITHIN A WEEK AT 4 DEGREES CELSIUS.

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.123	α = 90
b = 59.597	β = 93.37
c = 153.076	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	ADSC CCD		2009-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.9	45.53	96.8	0.103	14.25	3.47		30826		3	41.99

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	2.9	3	96.8		0.485	3.05	3.55

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 2V6M	2.9	45.47	1.99	30812	2039	96.84	0.1919	0.1878	0.19	0.2512	0.25

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]
-0.2486		-3.2788	1.8068		-1.5582

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.057
f_angle_d	1.704
f_chiral_restr	0.107
f_plane_restr	0.016
f_bond_d	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9135
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	54

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.