4IMD | pdb_00004imd

Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase trapped with pyruvate covalently bound through a Schiff base to Lys164

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	298	21% PEG1000, 0.15 M sodium chloride, 0.1 M sodium potassium phosphate, soaked in 0.05 M pyruvate for 24 hours, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.825	α = 90
b = 114.057	β = 111.74
c = 82.03	γ = 90

Symmetry
Space Group	P 1 21 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 315r		2008-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97946	SSRL	BL7-1

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	2.1	50	98.3	0.084	14	3.6	79123	79123	-3	-3

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	2.1	2.154	91.6		0.325	3.4	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	2.1	35.68	79123	75078	4045	98.16	0.18146	0.17949	0.1791	0.21847	0.2174	RANDOM	29.191

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]
2.05		0.32	0.46		-2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.913
r_dihedral_angle_4_deg	16.729
r_dihedral_angle_3_deg	15.447
r_dihedral_angle_1_deg	6.363
r_angle_refined_deg	1.919
r_chiral_restr	0.124
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9184
Nucleic Acid Atoms
Solvent Atoms	799
Heterogen Atoms	64

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling