3LCW | pdb_00003lcw

L-KDO aldolase complexed with hydroxypyruvate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NAL	PDB enrty 1NAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	2.0M ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.828	α = 90
b = 120.828	β = 90
c = 195.879	γ = 120

Symmetry
Space Group	P 32 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 QUANTUM 4r	vertically focusing mirror	2008-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1.0	SPring-8	BL12B2

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	2.35	30	99.9	0.064	34.4	6.1	69591	69521		1

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)
	2.35	2.43	100		0.623	3.7	6.1	6849

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	PDB enrty 1NAL	2.35	27.83	66318	62952	3366	90.6	0.23763	0.23763	0.2357	0.2273	0.2743	0.2667	RANDOM	44.495

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]
-0.715	-3.371		-0.715		1.43

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.724
c_scbond_it	1.907
c_mcangle_it	1.828
c_angle_deg	1.30856
c_mcbond_it	1.162
c_bond_d	0.006054

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8936
Nucleic Acid Atoms
Solvent Atoms	493
Heterogen Atoms	44

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing