1J4A

INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		MODEL OF NATIVE D-LDH WHICH IS CURRENTLY BEING DEPOSITED IN THE PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		Orthorhombic crystals were grown by vapour diffusion from solutions of 20 % PEG 6K, 0.2 M ammonium sulphate in 0.1 M cacodylate buffer pH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.3	α = 90
b = 188	β = 90
c = 193.4	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	MARRESEARCH	MIRRORS	1998-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	1.9	19	98.4	0.047	16.1	3.1		132348		-3	0.215

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)
	1.9	1.93	92.4		0.327	2.2

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 APART FROM THE LAST 3 CYCLES	MODEL OF NATIVE D-LDH WHICH IS CURRENTLY BEING DEPOSITED IN THE PDB	1.9	19	132346	6647	98.4	0.204	0.204	0.259	RANDOM	0.327

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
p_transverse_tor	36.1
p_staggered_tor	15
p_planar_tor	3.9
p_scangle_it	3.2
p_mcangle_it	2.5
p_scbond_it	2.5
p_mcbond_it	1.9
p_multtor_nbd	0.25
p_xhyhbond_nbd	0.197
p_xyhbond_nbd	0.197
p_singtor_nbd	0.19
p_chiral_restr	0.13
p_planar_d	0.035
p_angle_d	0.031
p_plane_restr	0.023
p_bond_d	0.013
p_angle_deg
p_hb_or_metal_coord
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10473
Nucleic Acid Atoms
Solvent Atoms	900
Heterogen Atoms	55

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling