3PV3 | pdb_00003pv3

Structure of Legionella fallonii DegQ (S193A variant)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PV2	PDB ENTRY 3PV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	292	22.5% (v/v) PEG 400, 100 mM glycine pH 9.5, vapor diffusion, sitting drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.03	α = 90
b = 155.03	β = 90
c = 260.6	γ = 120

Symmetry
Space Group	H 3

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	Rayonics MX-225 3x3 CCD		2010-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.1	119.351	98.7	0.095	6.6	2.9	41803	41803

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.27	99.4		0.455	0.455	1.7	2.9

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 3PV2	3.1	59.61	39691	2109	98.7	0.2277	0.22419	0.22	0.2919	0.29	RANDOM	72.179

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]
0.27	0.14		0.27		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.132
r_dihedral_angle_3_deg	21.928
r_dihedral_angle_4_deg	17.331
r_dihedral_angle_1_deg	6.79
r_angle_other_deg	4.432
r_scangle_it	1.851
r_angle_refined_deg	1.439
r_scbond_it	1.021
r_mcangle_it	0.977
r_mcbond_it	0.529
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11766
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing