5A29 | pdb_00005a29

Family 2 Pectate Lyase from Vibrio vulnificus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V8J	PDB ENTRY 2V8J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	CRYSTALS OF VVPL2 DEVELOPED VIA HANGING DROP VAPOUR DIFFUSION METHOD AT A PROTEIN CONCENTRATION OF 15 MG/ML BY MIXING EQUAL AMOUNTS OF THE PROTEIN SOLUTION WITH A MOTHER LIQUOR CONSISTING OF 16% (W/V) POLYETHYLENE GLYCOL 3,350, 0.14 M NA/K TARTRATE, AND 0.1 M HEPES (PH 7.0) AT 19 DEGREES CELSIUS. CRYSTALS WERE CRYOPROTECTED BY BRIEF CRYSTAL IMMERSION INTO A SOLUTION OF THE RESERVOIR SOLUTION SUPPLEMENTED WITH 25% ETHYLENE GLYCOL, AND SUBSEQUENTLY FROZEN IN A LIQUID NITROGEN STREAM PRIOR TO DIFFRACTION EXPERIMENTS.

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.102	α = 90
b = 141.102	β = 90
c = 72.426	γ = 120

Symmetry
Space Group	P 65

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	MIRRORS RH COATED	2013-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

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	122	99.8	0.1	29.1	4.8		64624

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	1.95	100		0.42	4.6	5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2V8J	1.9	122.2	61132	3266	99.59	0.1579	0.15585	0.16	0.19678	0.2	RANDOM	27.831

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]
-0.58	-0.29		-0.58		1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.292
r_dihedral_angle_4_deg	16.993
r_dihedral_angle_3_deg	13.36
r_dihedral_angle_1_deg	6.696
r_scbond_it	4.261
r_mcangle_it	3.681
r_mcbond_it	2.97
r_angle_refined_deg	1.907
r_chiral_restr	0.164
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
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	4526
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing