2PMA | pdb_00002pma

Structural Genomics, the crystal structure of a protein Lpg0085 with unknown function (DUF785) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	20% PEG1000, 0.2M MgCl2, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.711	α = 90
b = 81.855	β = 90
c = 97.993	γ = 90

Symmetry
Space Group	P 21 21 21

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	mirror	2006-08-03	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315	mirror	2007-03-05	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.14046	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.91956, 0.91976, 0.91279	APS	19-ID

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	1.89	37.77	99.7	0.045	52.7	7	27464	27464			24.8

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	1.89	1.93	97.5		0.234	8.2	6.3

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	MAD	THROUGHOUT	1.89	37.77	26024	26024	1381	99.68	0.18586	0.18439	0.18	0.21301	0.21	RANDOM	35.063

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]
-0.04			-0.03		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.279
r_dihedral_angle_4_deg	16.449
r_dihedral_angle_3_deg	15.916
r_dihedral_angle_1_deg	6.863
r_scangle_it	3.805
r_scbond_it	2.502
r_mcangle_it	1.698
r_angle_refined_deg	1.526
r_mcbond_it	1.036
r_nbtor_refined	0.31
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.123
r_symmetry_hbond_refined	0.12
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	2003
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing