3FRL | pdb_00003frl

The 2.25 A crystal structure of LipL32, the major surface antigen of Leptospira interrogans serovar Copenhageni

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	289	1.4 M trisodium citrate, 0.1 M HEPES, 20 mM triethanolamine-HCl, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4	69.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.725	α = 90
b = 126.725	β = 90
c = 95.996	γ = 120

Symmetry
Space Group	P 32 2 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	MARMOSAIC 225 mm CCD		2008-06-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.459, 0.97814, 0.97831	LNLS	W01B-MX2

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	2.25	40	99.4	0.071	22	10.5	42419	42419

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)
	2.25	2.33	95.8		0.466	1.9	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.25	35	40149	2129	99.38	0.18358	0.18134	0.2465	0.22712	0.2842	RANDOM	40.12

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]
2.33	1.17		2.33		-3.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.005
r_dihedral_angle_3_deg	15.989
r_dihedral_angle_4_deg	15.464
r_dihedral_angle_1_deg	6.822
r_scangle_it	2.237
r_scbond_it	1.764
r_angle_refined_deg	1.581
r_mcangle_it	1.12
r_angle_other_deg	0.925
r_mcbond_it	0.802
r_symmetry_vdw_other	0.287
r_symmetry_vdw_refined	0.262
r_nbd_other	0.207
r_nbd_refined	0.197
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.179
r_mcbond_other	0.179
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.097
r_nbtor_other	0.09
r_xyhbond_nbd_other	0.05
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3624
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	23

Software

Software
Software Name	Purpose
MAR345	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling