4J4B | pdb_00004j4b

PylD in complex with L-lysine-Ne-D-ornithine and NADH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SeMet-model; coordinates have not been deposited

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M TRIS; 27% PEG3350; 0.2 M Li2SO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.383	α = 90
b = 142.44	β = 90
c = 167.305	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	CCD	Bruker Platinum 135		2012-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	60	99.9	0.059	19.7	5.5	46157	46111	2	2

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	1.9	2	99.5		0.496	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SeMet-model; coordinates have not been deposited	1.9	10	43739	43739	2330	99.87	0.213	0.20703	0.20533	0.2	0.2399	0.24	RANDOM	35.879

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]
0.14			-0.77		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.634
r_sphericity_free	30.454
r_dihedral_angle_3_deg	15.656
r_dihedral_angle_4_deg	12.826
r_sphericity_bonded	5.708
r_dihedral_angle_1_deg	5.249
r_rigid_bond_restr	1.562
r_angle_refined_deg	1.203
r_chiral_restr	0.074
r_bond_refined_d	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3904
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	128

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
SCALEPACK	data scaling