3GP6 | pdb_00003gp6

Crystal structure of PagP in SDS/MPD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1THQ	PDB entry 1THQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	1M MPD, 0.1M citrate pH 5.6, 1.7M lithium sulphate, 0.3M ammonium sulphate, SDS, Phase separation, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.228	α = 90
b = 113.228	β = 90
c = 55.064	γ = 120

Symmetry
Space Group	P 62 2 2

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 315		2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98	APS	19-ID

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	1.4	20	97.7	0.068		8.2	40433	40433	-3	-3	21.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.42	80.4		0.531	1.36	4.1	1633

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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 entry 1THQ	1.4	20	-3	-3	39132	39132	1260	97.74	0.17259	0.17259	0.17147	0.17	0.20817	0.21	RANDOM	28.065

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]
3.2	1.6		3.2		-4.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.108
r_dihedral_angle_4_deg	18.014
r_sphericity_free	15.265
r_dihedral_angle_3_deg	13.991
r_sphericity_bonded	9.638
r_dihedral_angle_1_deg	7.084
r_scangle_it	5.134
r_scbond_it	4.125
r_mcangle_it	3.806
r_mcbond_it	2.793
r_rigid_bond_restr	2.612
r_angle_refined_deg	2.119
r_mcbond_other	1.726
r_angle_other_deg	0.96
r_xyhbond_nbd_refined	0.244
r_symmetry_vdw_other	0.242
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.222
r_metal_ion_refined	0.217
r_nbtor_refined	0.199
r_nbd_other	0.193
r_symmetry_vdw_refined	0.183
r_chiral_restr	0.137
r_symmetry_metal_ion_refined	0.105
r_nbtor_other	0.092
r_xyhbond_nbd_other	0.042
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1258
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	209

Software

Software
Software Name	Purpose
HKL-3000	data collection
EPMR	phasing
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling