1HKV

mycobacterium diaminopimelate dicarboxylase (lysa)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		4 UL HANGING DROPS (2 UL OF DAPDC 10 MG/ML CONTAINING 5MM OF LYSINE COMBINED WITH 2 UL OF WELL SOLUTION) WERE EQUILIBRATED AGAINST 500 UL OF WELL SOLUTION (24% PEG-MME 5K, 0.1M MES BUFFER PH6.3 AND 60 MM AMMONIUM SULFATE). THESE CRYSTALS WERE SOAKED FOR 3 HRS IN IN MOTHER LIQUOR CONTAINING 0.2 MM PLP. THE CRYSTALS ARE DISTINCTLY YELLOW., pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
3.9	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.452	α = 90
b = 111.452	β = 90
c = 238.253	γ = 90

Symmetry
Space Group	P 41 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	120	CCD	ADSC CCD	DOUBLE MONO	2002-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B		APS	14-ID-B

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	2.6	65.5	99.8	0.081	14.6	6.2		44373

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	2.6	2.67	94		0.405	3.1	6.2

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	PDB ENTRY 1HKW	2.6	18	44373	2374	99.8	0.227	0.224	0.268	RANDOM	47.48

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]
-0.08			-0.08		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.95
r_scangle_it	4.474
r_scbond_it	2.805
r_mcangle_it	2.042
r_angle_refined_deg	1.552
r_symmetry_hbond_refined	1.348
r_mcbond_it	1.132
r_angle_other_deg	0.858
r_nbd_other	0.259
r_symmetry_vdw_other	0.239
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.159
r_chiral_restr	0.116
r_nbtor_other	0.1
r_bond_refined_d	0.03
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6660
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
EPMR	phasing