3BDD | pdb_00003bdd

CRYSTAL STRUCTURE OF A PUTATIVE MULTIPLE ANTIBIOTIC-RESISTANCE REPRESSOR (SSU05_1136) FROM STREPTOCOCCUS SUIS 89/1591 AT 2.20 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	277	NANODROP, 0.2M NaCl, 20.0% PEG 8000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.734	α = 90
b = 100.43	β = 111.42
c = 68.695	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2007-08-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0000, 0.9798	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	15.895	95.6	0.066	0.066	7.9	1.9		31068			37.26

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	2.2	2.32	97.1		0.417	0.417	1.7	1.9	4574

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	2.2	15.895	31066	1581	95.45	0.225	0.223	0.23	0.275	0.28	RANDOM	39.499

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]
0.51		0.16	-0.35		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.684
r_dihedral_angle_3_deg	10.745
r_dihedral_angle_4_deg	10.545
r_scangle_it	4.372
r_dihedral_angle_1_deg	3.131
r_scbond_it	3.07
r_angle_refined_deg	1.411
r_mcangle_it	1.288
r_angle_other_deg	1.275
r_mcbond_it	0.977
r_mcbond_other	0.199
r_nbd_refined	0.15
r_nbtor_refined	0.133
r_symmetry_vdw_other	0.13
r_nbd_other	0.111
r_xyhbond_nbd_refined	0.084
r_chiral_restr	0.081
r_nbtor_other	0.071
r_symmetry_hbond_refined	0.057
r_symmetry_vdw_refined	0.055
r_bond_refined_d	0.012
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4333
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing