2HFB | pdb_00002hfb

Crystal structure of selenomethionine-labelled RafE from Streptococcus pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.1	295	1.8M Ammonium sulfate, 0.1M Na citrate pH 5.1, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.538	α = 90
b = 144.538	β = 90
c = 224.082	γ = 120

Symmetry
Space Group	P 61 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 4		2004-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.9792	SRS	PX14.2

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	2.9	29.51	100	0.083	15.2	11.54		57961

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	2.9	3	100		0.417	5.4	11.56	5783

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.9	29.51	31023	1568	99.18	0.25	0.248	0.2439	0.29	0.2891	RANDOM	75.269

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	42.554
r_dihedral_angle_3_deg	23.485
r_dihedral_angle_4_deg	19.57
r_mcbond_other	18.932
r_dihedral_angle_1_deg	8.88
r_scangle_it	7.495
r_mcangle_it	7.065
r_scbond_it	4.789
r_angle_other_deg	4.42
r_mcbond_it	4.243
r_angle_refined_deg	2.239
r_symmetry_hbond_refined	0.429
r_symmetry_vdw_refined	0.387
r_nbd_other	0.296
r_symmetry_vdw_other	0.283
r_nbd_refined	0.279
r_nbtor_refined	0.215
r_chiral_restr	0.213
r_xyhbond_nbd_refined	0.201
r_nbtor_other	0.13
r_xyhbond_nbd_other	0.074
r_bond_refined_d	0.022
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6042
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	1

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction