2V7P

Crystal structure of lactate dehydrogenase from Thermus Thermophilus HB8 (Holo form)

X-RAY DIFFRACTION

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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		6		0.1M MES PH 6, 15% PEG 6K, 10MM NADH, 5MM OXAMATE

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.5	α = 90
b = 142.85	β = 90
c = 59.57	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	MARRESEARCH	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	40	97.7	0.1	10.6	4.86		74676		-3	15

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	2.15	96.7		0.34	3.78	3.59

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2V6M	2.1	39.16	74676	3733	97.7	0.192	0.192	0.204	RANDOM	25.1

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]
2.05			-4.06		2.01

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.2
c_scangle_it	2.67
c_improper_angle_d	1.93
c_scbond_it	1.85
c_mcangle_it	1.82
c_angle_deg	1.3
c_mcbond_it	1.29
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9043
Nucleic Acid Atoms
Solvent Atoms	535
Heterogen Atoms	200

Software

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