2V6B

Crystal structure of lactate dehydrogenase from Deinococcus Radiodurans (apo form)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LDN	PDB ENTRY 1LDN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		9		0.1M BICINE PH 9, 20% PEG 5K MME

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.35	α = 90
b = 127.93	β = 90
c = 72.92	γ = 90

Symmetry
Space Group	P 21 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	100	CCD	MARRESEARCH	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.5	20	98.9	0.06	17.06	4.35		40233		-3	41.6

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	2.5	2.55	94.6		0.46	3.12	4.28

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 1LDN	2.5	19.83	40233	2012	99.1	0.23	0.23	0.25	RANDOM	51

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]
2.35			-5.45		3.1

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.1
c_scangle_it	4.34
c_mcangle_it	3.32
c_scbond_it	2.97
c_mcbond_it	2.03
c_angle_deg	1.1
c_improper_angle_d	0.89
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	8218
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms

Software

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